Methods for rapid antimicrobial susceptibility testing

ABSTRACT

The present invention relates, in part, to methods and kits for rapidly determining antimicrobial susceptibility of microorganisms.

RELATED APPLICATIONS

This application is a continuation application of U.S. patentapplication Ser. No. 15/464,240, filed on Mar. 20, 2017, now U.S. Pat.No. 9,834,808, which is a continuation of International PatentApplication No. PCT/US17/14343 filed Jan. 20, 2017. PCT/US17/14343designates the United States and claims priority to and benefit of U.S.Provisional Patent Application No. 62/281,698, filed Jan. 21, 2016; U.S.Provisional Patent Application No. 62/298,821, filed Feb. 23, 2016; U.S.Provisional Patent Application No. 62/326,545, filed Apr. 22, 2016; U.S.Provisional Patent Application No. 62/338,376, filed May 18, 2016; U.S.Provisional Patent Application No. 62/370,579, filed Aug. 3, 2016; andU.S. Provisional Patent Application No. 62/383,198, filed Sep. 2, 2016.The contents of the aforementioned patent applications are incorporatedherein by reference in their entireties.

BACKGROUND OF THE INVENTION

Antimicrobial-resistant microbial infections are associated with poorclinical outcomes including increased morbidity, mortality, andhealthcare costs among infected patients. The prevalence of theseorganisms in such facilities in the United States has steadily increasedover the last 30 years. Phenotypic antimicrobial susceptibility testing(AST) of microorganisms is critical for informing physicians ofappropriate therapeutic regimens. Using current methods, ASTdetermination typically requires a minimum of eight hours, rendering itan overnight process due to shift work in many clinical microbiologylaboratories. While awaiting a determination from current AST methods,patients are often administered broad-spectrum antimicrobials whichoften have significant detrimental effects on patient health and/orcontribute to the growing antimicrobial resistance epidemic.Furthermore, this time delay to getting accurate antimicrobial treatmentinformation increases patient stays in hospitals, thereby increasingcosts and inconvenience to the patient.

Accordingly, a need exists for a method that rapidly determinesantimicrobial susceptibility of a microbial infection. The methoddescribed here is further advantageous in that it addresses this need ina cost-effective manner because it is compatible with existing assayhardware components.

SUMMARY OF THE INVENTION

The present invention permits rapid determination of antibioticsusceptibility of microbial infections. The invention is based in partupon the surprising discovery of non-specific surface binding assaysthat provide accurate and rapid Antimicrobial Susceptibility Testing(AST) determinations in fewer than twelve hours—and, specifically, underfour hours. The present invention (“Fast-AST”) provides accurate resultsthat are consistent with results obtained using the Clinical LaboratoryStandards Institute (CLSI) reference methods when tested with multipleantimicrobials and on a plurality of microorganisms; however, thepresent invention takes significantly less time to obtain results thanthe CLSI methods. Moreover, the present invention accuratelydifferentiates an antimicrobial's MIC for clinically-relevant microbialstrains that are resistant to one or more antimicrobials and theantimicrobial's MIC for strains of the same microorganism that aresensitive to the antimicrobials. Furthermore, the present invention mayinclude signaling agents (e.g., Europium compounds) that are bound tomicroorganisms non-specifically rather than specifically (e.g., viachemically conserved groups or biochemically conserved binding sites onmicroorganisms), thereby expanding the generalization of the presentinvention to any microorganism and allowing onset of an appropriatetreatment without first needing to identify the particular infectiousmicroorganism. Also, the present invention permits signal amplificationsuch that microbes may be rapidly detected at lower concentrations.e.g., from a dilute culture of microorganisms or via a patient'sbiological sample. Additionally, the present invention may use Europiumformulations as chemical moiety, thereby expanding the dynamic range ofthe methods and allowing for more accurate determinations from a rangeof microbial samples. Finally, the present invention is compatible withexisting equipment, thereby enabling rapid adoption in current clinicallaboratories. Accordingly, the present invention, in a greatly reducedamount of time and expense, relative to standard methods, can provide apatient with an appropriate treatment regimen, i.e., a specificantimicrobial and at a particular dosage. Thus, the present inventionwill improve patient outcomes, lower hospital costs, and help reducefurther evolution of antimicrobial resistant microorganisms; thus, thepresent invention represents a significant breakthrough in the ASTfield.

An aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in thepresence of an antimicrobial and a signaling agent, which is capable ofbinding to a surface of the microorganisms, under conditions thatpromote growth of the microorganisms; separating the microorganismsbound by the signaling agent from the unbound signaling agent; anddetermining signal levels associated with the microorganisms as comparedto one or more controls.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in thepresence of an antimicrobial under conditions that promote growth of themicroorganisms; adding a signaling agent capable of binding to a surfaceof the microorganisms; separating the microorganisms bound by thesignaling agent from the unbound signaling agent; and determining signallevels associated with the microorganisms as compared to one or morecontrols.

Yet another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in a cartridgeincluding a plurality of chambers, each chamber containing one or moreantimicrobials, under conditions that promote growth of themicroorganisms; adding a signaling agent, which is capable of binding toa surface of the microorganisms, to the plurality of chambers; removingunbound signaling agent; and determining signaling levels in theplurality of chambers as compared to one or more controls.

An aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includesincubating microorganisms in the presence of an antimicrobial and asignaling agent, which includes a signal amplifier and one or morechemical moieties capable of binding non-specifically to a surface ofthe microorganisms, under conditions that promote growth of themicroorganisms; separating the microorganisms bound by the signalingagent from the unbound signaling agent; and determining signal levelsassociated with the microorganisms as compared to one or more controls.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includesincubating microorganisms in the presence of an antimicrobial underconditions that promote growth of the microorganisms; adding a signalingagent including a signal amplifier and one or more chemical moietiescapable of binding non-specifically to a surface of the microorganisms;separating the microorganisms bound by the signaling agent from theunbound signaling agent; and determining signal levels associated withthe microorganisms as compared to one or more controls.

Yet another aspect of the present invention is a kit for determiningantimicrobial susceptibility of microorganisms. The kit includes asignaling agent capable of binding to a surface of the intactmicroorganisms of interest; a solution for incubating a samplecontaining microorganisms; and one or more reagents for generatingsignals from the signaling agent.

Any aspect or embodiment described herein can be combined with any otheraspect or embodiment as disclosed herein. While the disclosure has beendescribed in conjunction with the detailed description thereof, theforegoing description is intended to illustrate and not limit the scopeof the disclosure, which is defined by the scope of the appended claims.Other aspects, advantages, and modifications are within the scope of thefollowing claims.

The patent and scientific literature referred to herein establishes theknowledge that is available to those with skill in the art. All UnitedStates patents and published or unpublished United States patentapplications cited herein are incorporated by reference. All publishedforeign patents and patent applications cited herein are herebyincorporated by reference. All other published references, documents,manuscripts and scientific literature cited herein are herebyincorporated by reference.

Other features and advantages of the invention will be apparent from theDrawings and the following detailed description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and further features will be more clearly appreciated from thefollowing detailed description when taken in conjunction with theaccompanying drawings. The drawings however are for illustrationpurposes only; not for limitation.

FIG. 1 is a schematic showing generalized steps of the presentinvention.

FIG. 2A to FIG. 2D are graphs and illustrations showing key features ofaspects of the present invention (“fast-AST”).

FIG. 3 is a schematic comparing steps required in currently-usedAntimicrobial Susceptibility Testing (AST) systems and aspects of thepresent invention.

FIG. 4 is a graph showing the time delay required to obtain resultsusing a currently-used AST system (i.e., BioMeriéux's Vitek2).

FIG. 5 is a graph showing a comparison of a minimum inhibitoryconcentration (MIC) determination of clindamycin on Staphylococcusaureus (ATCC strain 29213) using the present invention (“fast-AST”technique) and a standard, overnight growth followed by optical density(OD) reading at 600 nm. The data shown for the “fast-AST” is from thefive minute point after the start of incubation with detection solutionand represents the average and standard deviations of four wells, withvalues for each assay type relative to an antimicrobial-free control.

FIG. 6 is a graph showing a comparison of a MIC determination ofceftazidime on Pseudomonas aeruginosa (ATCC strain 27853) using thepresent invention (“fast-AST” technique) and a standard, overnightgrowth followed by optical density (OD) reading at 600 nm. The datashown represents the average and standard deviations of four wells, withvalues for each assay type relative to an antimicrobial-free control.

FIG. 7 is a graph showing a MIC determination comparison using thepresent invention (“fast-AST”) for two strains of Pseudomonasaeruginosa: a susceptible strain (ATCC strain 27853) and a resistantstrain (ATCC strain BAA-2108). The data shown represents the average offour wells, with values for each assay relative to an antimicrobial-freecontrol.

FIG. 8 is a table summarizing data from Example 2. It compares MIC callsby the “fast-AST” technique with those of the standard overnight OD₆₀₀procedure. The data shown represents the average of four wells, withvalues for each assay type relative to an antimicrobial-free control.

FIG. 9 is a graph showing a comparison of raw optical signal vs.Staphylococcus aureus concentration (in CFU/ml) for two techniques: thepresent invention (“fast-AST” amplification technique) and the standardoptical density at 600 nm technique (OD₆₀₀).

FIG. 10 is a graph showing the MIC results for the present invention(the “fast-AST” method) compared to the Clinical Laboratory StandardsInstitute (CLSI) reference method for seven pathogenic bacterialspecies.

FIG. 11 is a table identifying the bacteria, antimicrobials, and thesignaling agent/chemical moiety used in Example 4.

FIG. 12A to FIG. 12C are tables showing representative SensiTitre®results for S. aureus (FIG. 12A) and K. pneumonia (FIG. 12B). Data isnot presented using the present invention for the nitrofurantonin S.aureus experiment because only two wells were dedicated to thisantimicrobial.

FIG. 13A to FIG. 13C is a graph showing a comparison between MIC resultsobtained by the present invention and the CLSI reference method for theantimicrobials oxacillin (FIG. 13A), vancomycin (FIG. 13B), andlevofloxacin (FIG. 13C) on S. aureus clinical strains.

FIG. 14A to FIG. 14D is a graph showing a comparison between MIC resultsobtained by the present invention and the CLSI reference method for theantimicrobials ampicillin (FIG. 14A), ciprofloxacin (FIG. 14B), imipenem(FIG. 14C), and gentamicin (FIG. 14D) on E. coli clinical strains.

FIG. 15 is a graph showing that the present invention (“fast-AST”)consistently produces MIC results similar to those obtained by the CLSIstandard reference method over the course of one month on the sameclinical species of S. aureus.

FIG. 16 to FIG. 23 are graphs comparing sensitives for a plurality ofantimicrobials for a chemically sensitive E. coli strain (“QC 25922”)and a clinically-relevant antimicrobial-resistant strain (“Clinical”).The antimicrobials used are Imipenem (FIG. 16); Ampicillin (FIG. 17):Ceftazidime (FIG. 18); Gentamicin (FIG. 19); Levofloxacin (FIG. 20);Trimethethoprim/Sulfamethoxazole (SXT) (FIG. 21): Ciprofloxacin (FIG.22); and Cetriaxone (FIG. 23).

FIG. 24 to FIG. 26 are graphs comparing sensitives for a plurality ofantimicrobials for a chemically sensitive S. aureus (“QC strain 29213”)strain. The antimicrobials used are Vancomycin (FIG. 24): Penicillin(FIG. 25); and Teicoplanin (FIG. 26).

FIG. 27 and FIG. 28 are graphs showing MIC results using a method of thepresent invention directly on a clinical sample and compared to clinicalresults obtained with a Beckman-Coulter MicroScan Walkaway (in which asub-culturing step is performed prior to overnight growth).

FIG. 29 is a graph showing the detected fluorescence (via a signalingagent comprising Europium and use of wheat germ agglutinin, whichspecifically binds gram positive bacteria) of a gram-positive bacterialsolution relative to the concentration of bacteria in the solution.

FIG. 30 is a graph showing the detected fluorescence (via a signalingagent comprising Europium and use of Polymixin B, which specificallybinds gram negative bacteria) of a gram-negative bacterial solutionrelative to the concentration of bacteria in the solution.

FIG. 31 are graphs that compare MIC values obtained when anantibody-bound Europium formulation is used as signaling agent to MICvalues obtained when an antibody-horse radish peroxidase (HRP) is usedas signaling agent. The MIC for SXT for this clinical S. aureus strainwas ≤0.5 μg/ml by CLSI overnight method.

FIG. 32 are graphs showing the relative fluorescence units (RFU)obtained for specific bacterial concentrations for two Europiumformulations that are non-specifically bound to bacterial surfaces.

FIG. 33 are graphs showing the RFU obtained for specific bacterialconcentrations of two bacterial species for two Europium formulationsthat are non-specifically bound to bacterial surfaces.

FIG. 34 and FIG. 35 are graphs showing the RFU obtained for specificbacterial concentrations of various bacterial species for a Europiumformulation that is non-specifically bound to bacterial surfaces.

FIG. 36A to FIG. 36C are graphs showing the RFU obtained for specificbacterial concentrations of various bacterial species for a Europiumformulation that is non-specifically bound to bacterial surfaces whenusing various washes comprising glutaraldehyde.

FIG. 37 are graphs showing the RFU obtained for specific bacterialconcentrations of E. coli for a Europium formulation that isnon-specifically bound to bacterial surfaces using a two-step processcomprising NH2-PEG-Biotin followed by streptavidin-europium (Eu-SAv).

FIG. 38 is a graph showing the RFU obtained for specific bacterialconcentrations of E. coli for a Europium formulation that isnon-specifically bound to bacterial surfaces using a two-step processcomprising NHS-LC-LC-Biotin followed by Eu-SAv.

FIG. 39 is a schematic that illustrates the confounding effect thatfilamentous growth has on volumetric-based determinations ofmicroorganism's antimicrobial susceptibilities. Susceptible bacteriaentering filamentous growth may appear falsely resistant due to theirincreased volume.

FIG. 40 is a schematic that illustrates a method for minimizing theinterference of filamentous microorganisms in AST determinations.

FIG. 41 is a graph showing the result of an assay using signaling agentcomprising a fluorescent nanoparticle for E. coli andampicillin-resistant E. coli treated with and without 100 μg/mlampicillin (a concentration well above the MIC).

FIG. 42 is a graph showing the result of an assay using signaling agentcomprising a fluorescent nanoparticle for E. coli and with varyingampicillin concentrations. Error bars shows the standard deviation ofthree replicates.

FIG. 43 is a graph showing the ability of E. coli-functionalizedmagnetic beads are capable of binding and isolating intact bacteriumfrom a solution.

FIG. 44 is a graph showing the number of intact bacteria that areisolated by functionalized magnetic beads from solutions comprisingvarying amounts of an antimicrobial.

FIG. 45 includes graphs comparing the number of intact bacteria that areisolated by centrifugation versus functionalized magnetic beads fromsolutions comprising varying amounts of an antimicrobial (here,vancomycin “VAN”). The MIC for VAN for this clinical S. aureus strainwas 8 μg/ml by CLSI overnight method.

FIG. 46A to FIG. 46C show tetra-amino metalorganic ligand (TAML®)nanolabel design and performance. FIG. 46A is a schematic showingnanolabel constituents. FIG. 46B is a graph showing catalytic comparisonof HRP and TAML (inset): the dashed lines are linear best fits for eachdataset with R2 of 0.997 for HRP and 0.987 for TAML. FIG. 46C is a graphshowing the TAML nanolabel vs. HRP comparison for C. difficile Toxin Aimmunoassay. In FIG. 46B and FIG. 46C, the signals were normalized to“1” at zero concentration, errors were propagated, and error barsrepresent ±1 standard deviation. Experiments were repeated three timesin triplicate with similar results.

DEFINITIONS

In order for the present invention to be more readily understood,certain terms are first defined below. Additional definitions for thefollowing terms and other terms are set forth throughout theSpecification.

As used in this Specification and the appended claims, the singularforms “a,” “an” and “the” include plural referents unless the contextclearly dictates otherwise.

Unless specifically stated or obvious from context, as used herein, theterm “or” is understood to be inclusive and covers both “or” and “and”.

The terms “e.g.,” and “i.e.” as used herein, are used merely by way ofexample, without limitation intended, and should not be construed asreferring only those items explicitly enumerated in the specification.

The terms “one or more”. “at least one”, “more than one”, and the likeare understood to include but not be limited to at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,140, 141, 142, 143, 144, 145, 146, 147, 148, 149 or 150, 200, 300, 400,500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000 or more and anynumber in between.

Conversely, the term “no more than” includes each value less than thestated value. For example, “no more than 100 nucleotides” includes 100,99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 89, 88, 87, 86, 85, 84, 83, 82,81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67, 66, 65, 64,63, 62, 61, 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46,45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28,27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10,9, 8, 7, 6, 5, 4, 3, 2, 1, and 0 nucleotides.

The terms “plurality”, “at least two”, “two or more”. “at least second”,and the like, are understood to include but not limited to at least 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137,138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149 or 150, 200,300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000 or moreand any number in between.

Throughout the specification the word “comprising,” or variations suchas “comprises” or “comprising,” will be understood to imply theinclusion of a stated element, integer or step, or group of elements,integers or steps, but not the exclusion of any other element, integeror step, or group of elements, integers or steps.

Unless specifically stated or obvious from context, as used herein, theterm “about” is understood as within a range of normal tolerance in theart, for example within 2 standard deviations of the mean. “About” canbe understood to be within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%,0.5%, 0.1%, 0.05%, 0.01%, or 0.001% of the stated value. Unlessotherwise clear from the context, all numerical values provided hereinare modified by the term “about”.

A surface can be an external surface of cell wall, cell envelope, plasmamembrane, or cell capsule: internal surface of cell wall, cell envelope,plasma membrane, or cell capsule; or within a cell wall, cell envelope,plasma membrane, or cell capsule. The surface may include structures ofthe cell projecting extracellularly, including but not limited tocilium, pilus, and flagellum. The surface may include an organelle. Thesurface may include transmembrane proteins, cell-wall proteins,extracellular proteins, intracellular proteins, extracellular-associatedpolysaccharides, intracellular-associated polysaccharides, extracellularlipids, intracellular lipids, membrane lipids, cell-wall lipids,proteins, polysaccharides, and/or lipids integral to or associated witha cell envelop. The surface may include a nucleic acid.

The surface may include a biomolecule to which the signaling agent bindsor associates. Exemplary biomolecules include peptidoglycans, mureins,mannoproteins, porins, beta-glucans, chitin, glycoproteins,polysaccharides, lipopolysaccharides, lipooligosaccharides,lipoproteins, endotoxins, lipoteichoic acids, teichoic acids, lipid A,carbohydrate binding domains, efflux pumps, other cell-wall and/orcell-membrane associated proteins, other anionic phospholipids, and acombination thereof.

Growth, as in growth of microorganisms, includes a proliferation innumber, an increase in length, an increase in volume, and/or an increasein nucleic acid and/or protein content of the microorganisms.

Controls may include antimicrobials for which the microorganism are notsusceptible. As examples, if the assay is used to determine thesusceptibility of gram-positive bacteria, then the controls (and thetest incubations) may include one or more antimicrobials that targetgram-negative bacteria and if the assay is used to determine thesusceptibility of eukaryotic microorganisms, the control (and the testincubations) may include one or more antibacterial antimicrobials.

A control may be a positive control measured from microorganisms underotherwise identical conditions but without antimicrobials or with one ormore antimicrobials for which the microorganisms are not susceptible.

A control may be measured from microorganisms under otherwise identicalconditions but without nutrients.

A control may be measured from microorganisms under otherwise identicalconditions with one or more toxins known to inhibit growth of themicroorganisms.

Controls may be historic controls. Here, the test incubations may beperformed after control incubations have been performed.

Alternately, controls may be performed in a cartridge distinct from thecartridge comprising the test incubations.

By “processed” is meant a step that isolates microorganisms from abiological sample, a step that increases the concentration ofmicroorganisms obtained from a biological sample, and/or a step thatincreases the number of microorganisms obtained from a biologicalsample, e.g., by culturing the microorganisms under conditions thatpromote proliferation of the microorganisms.

Compounds of this invention include those described generally herein,and are further illustrated by the classes, subclasses, and speciesdisclosed herein. As used herein, the following definitions shall applyunless otherwise indicated. For purposes of this invention, the chemicalelements are identified in accordance with the Periodic Table of theElements, CAS version. Handbook of Chemistry and Physics, 75th Ed.Additionally, general principles of organic chemistry are described in“Organic Chemistry”, Thomas Sorrell, University Science Books.Sausalito: 1999, and “March's Advanced Organic Chemistry”, 5th Ed., Ed.:Smith, M. B. and March, J., John Wiley & Sons, New York: 2001, theentire contents of which are hereby incorporated by reference.

The term “heterocycle”, “heterocyclyl”, or “heterocyclic” as used hereinmeans nonaromatic, monocyclic, bicyclic, or tricyclic ring systems inwhich one or more ring members are an independently selected heteroatom.In some embodiments, the “heterocycle”, “heterocyclyl”, or“heterocyclic” group has three to fourteen ring members in which one ormore ring members is a heteroatom independently selected from oxygen,sulfur, nitrogen, or phosphorus, and each ring in the system contains 3to 7 ring members.

The term “heteroatom” refers to one or more of oxygen, sulfur, nitrogen,phosphorus, and silicon (including, any oxidized form of nitrogen,sulfur, phosphorus, or silicon: the quaternized form of any basicnitrogen or; a substitutable nitrogen of a heterocyclic ring, forexample N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl) orNR+ (as in N-substituted pyrrolidinyl)).

The term “alkoxy”, or “thioalkyl”, as used herein, refers to an alkylgroup, as previously defined, attached through an oxygen (“alkoxy”) orsulfur (“thioalkyl”) atom.

The terms “haloalkyl”, “haloalkenyl”, “haloaliphatic”, and “haloalkoxy”mean alkyl, alkenyl or alkoxy, as the case may be, substituted with oneor more halogen atoms. This term includes perfluorinated alkyl groups,such as —CF3 and —CF2CF3.

The terms “halogen”, “halo”, and “hal” mean F, Cl, Br, or I.

The terms “aryl” and “ar-”, used alone or as part of a larger moiety,e.g., “aralkyl”, “aralkoxy”, or “aryloxyalkyl”, refer to an optionallysubstituted C6-14aromatic hydrocarbon moiety comprising one to threearomatic rings. For example, the aryl group is a C6-10aryl group (i.e.,phenyl and naphthyl). Aryl groups include, without limitation,optionally substituted phenyl, naphthyl, or anthracenyl. The terms“aryl” and “ar-”, as used herein, also include groups in which an arylring is fused to one or more cycloaliphatic rings to form an optionallysubstituted cyclic structure such as a tetrahydronaphthyl, indenyl, orindanyl ring. The term “aryl” may be used interchangeably with the terms“aryl group”, “aryl ring”, and “aromatic ring”.

The compounds of this invention can exist in free form for treatment, orwhere appropriate, as a pharmaceutically acceptable salt.

As used herein, the term “aromatic” includes aryl and heteroaryl groupsas described generally below and herein

The term “aliphatic” or “aliphatic group”, as used herein, means anoptionally substituted straight-chain or branched C1-12 hydrocarbonwhich is completely saturated or which contains one or more units ofunsaturation. For example, suitable aliphatic groups include optionallysubstituted linear or branched alkyl, alkenyl, and alkynyl groups.Unless otherwise specified, in various embodiments, aliphatic groupshave 1-12, 1-10, 1-8, 1-6, 1-4, 1-3, or 1-2 carbon atoms. It is apparentto a skilled person in the art that in some embodiments, the “aliphatic”group described herein can be bivalent.

The term “alkyl”, used alone or as part of a larger moiety, refers to asaturated, optionally substituted straight or branched chain hydrocarbongroup having 1-12, 1-10, 1-8, 1-6, 1-4, 1-3, or 1-2 carbon atoms.

The term “alkenyl”, used alone or as part of a larger moiety, refers toan optionally substituted straight or branched chain hydrocarbon grouphaving at least one double bond and having 2-12, 2-10, 2-8, 2-6, 2-4, or2-3 carbon atoms.

The term “alkynyl”, used alone or as part of a larger moiety, refers toan optionally substituted straight or branched chain hydrocarbon grouphaving at least one triple bond and having 2-12, 2-10, 2-8, 2-6, 2-4, or2-3 carbon atoms.

Unless otherwise stated, structures depicted herein are also meant toinclude all isomeric (e.g., enantiomeric, diastereomeric, and geometric(or conformational)) forms of the structure; for example, the R and Sconfigurations for each asymmetric center, (Z) and (E) double bondisomers, and (Z) and (E) conformational isomers. Therefore, singlestereochemical isomers as well as enantiomeric, diastereomeric, andgeometric (or conformational) mixtures of the present compounds arewithin the scope of the invention. Unless otherwise stated, alltautomeric forms of the compounds of the invention are within the scopeof the invention. Additionally, unless otherwise stated, structuresdepicted herein are also meant to include compounds that differ only inthe presence of one or more isotopically enriched atoms. For example,compounds having the present structures where there is a replacement ofhydrogen by deuterium or tritium, or a replacement of a carbon by a 13C-or 14C-enriched carbon are within the scope of this invention. Suchcompounds are useful, as a nonlimiting example, as analytical tools orprobes in biological assays:

It is to be understood that, when a disclosed compound has at least onechiral center, the present invention encompasses one enantiomer ofinhibitor free from the corresponding optical isomer, racemic mixture ofthe inhibitor and mixtures enriched in one enantiomer relative to itscorresponding optical isomer. When a mixture is enriched in oneenantiomer relative to its optical isomers, the mixture contains, forexample, an enantiomeric excess of at least 50%, 75%, 90%, 95% 99% or99.5%.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this application belongs and as commonly used in theart to which this application belongs; such art is incorporated byreference in its entirety. In the case of conflict, the presentSpecification, including definitions, will control.

DETAILED DESCRIPTION OF THE INVENTION

The present invention permits rapid determination of antibioticsusceptibility of microbial infections. The invention is based in partupon the surprising discovery of non-specific surface binding assaysthat provide accurate and rapid Antimicrobial Susceptibility Testing(AST) determinations in fewer than twelve hours—and, specifically, underfour hours. The present invention (“fast-AST”) provides accurate resultsthat are consistent with results obtained using the Clinical LaboratoryStandards Institute (CLSI) reference methods and when tested withmultiple antimicrobials and on a plurality of microorganisms: however,the present invention takes significantly less time to obtain resultsthan the CLSI methods. Moreover, the present invention accuratelydifferentiates an antimicrobial's MIC for clinically-relevant microbialstrains that are resistant to one or more antimicrobials and theantimicrobial's MIC for strains of the same microorganism that aresensitive to the antimicrobials. Furthermore, the present invention mayinclude signaling agents (e.g., Europium compounds) that are bound tomicroorganisms non-specifically rather than specifically (e.g., viachemically conserved groups or biochemically conserved binding sites onmicroorganisms), thereby expanding the generalization of the presentinvention to any microorganism and allowing onset of an appropriatetreatment without first needing to identify the particular infectiousmicroorganism. Also, the present invention permits signal amplificationsuch that microbes may be rapidly detected at lower concentrations,e.g., from a dilute culture of microorganisms or via a patient'sbiological sample. Additionally, the present invention may use Europiumformulations as chemical moiety, thereby expanding the dynamic range ofthe methods and allowing for more accurate determinations from a rangeof microbial samples. Finally, the present invention is compatible withexisting equipment, thereby enabling rapid adoption in current clinicallaboratories. Accordingly, the present invention, in a greatly reducedamount of time and expense, relative to standard methods, can provide apatient with an appropriate treatment regimen, i.e., a specificantimicrobial and at a particular dosage. Thus, the present inventionwill improve patient outcomes, lower hospital costs, and help reducefurther evolution of antimicrobial resistant microorganisms; thus, thepresent invention represents a significant breakthrough in the ASTfield.

Aspects of the present invention deliver accurate, low-cost phenotypicAST results by chemically amplifying microorganism surfaces. This novelapproach offers two primary advances over currently-used methods: 1)Quantification of microorganism growth by determining relative surfacearea, which overcomes limitations of current platforms with regard tofilamentous growth regimes, as are well known to those skilled in theart; and 2) Microorganism amplification with optimal sensitivity in the1×10³ to 1×10⁸ CFU/ml range using standard optical detection equipment.

As disclosed herein (e.g., in the Examples), the present invention hasbeen shown to deliver equivalent results to the gold-standard for abroad range of microorganism species, including all six (Enterococcusfaecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacterbaumannii. Pseudomonas aeruginosa, and Enterobacter species) (“ESKAPE”)pathogens. Because of the generality of the present invention, it isflexible, in that it can be easily and cheaply adapted to newmicroorganism species strains and diagnostic tests.

The present invention provides low-cost, phenotypic ASTs from standardmicrobial colony isolates or from direct-from-positive blood samples, inless than 8 hours, preferably less than 5 hours. This allows standardclinical microbiology laboratories same-shift, phenotypic AST results.The below working Examples demonstrate that chemical amplification ofmicroorganism surfaces produces accurate minimum inhibitoryconcentration (MIC) and breakpoint calls in less than four hours. Thiswill shorten current wait times by over twenty hours and will matchdirect-from-positive blood culture MALDI-TOF identifications currentlynearing FDA trials, as well as direct-from-positive blood culturemultiplex PCR identification platforms that have already obtained FDAclearance. This design enables the present invention (“fast-AST”platform) to break the traditional speed vs. cost tradeoff. The presentinvention is compatible both with standard microplate formats (e.g.,having 6, 12, 24, 48, 96, 384, or 1536 wells) and conventional opticaldetectors.

Identification and antimicrobial susceptibility testing (AST) of theinvading pathogen with speed and accuracy allow for timelyadministration of the most effective therapeutic agent. Such treatmentameliorates the infection, decreases length of stay for hospitalizedpatients, and diminishes the time patients are subject to broad spectrumantimicrobials, the latter contributing the global epidemic ofantimicrobial resistance. In contrast, the currently-accepted overthirty hour wait for microorganism identification and susceptibilityresults necessitates overuse of broad-spectrum antimicrobials and longerthan necessary patient stay. For this reason, the Presidential AdvisoryCouncil on Combating Antibiotic-Resistant Bacteria recently made thedevelopment and use of rapid diagnostics for the detection of antibioticresistant bacteria one of its main goals.

The present invention, which generates more rapid and accurate ASTdeterminations, may provide actual cost benefits of over $2,000 perpatient. These value points include the more easily quantifiable(reduced length of stay and expensive treatments) and the moreintangible, difficult to value (patient mortality and societal impactsfrom improved antimicrobial stewardship). Some of these intangiblevalues, such as the value of antimicrobial stewardship, may become morequantified as regulatory bodies start to impose costs on hospitals fornot adopting more rigorous antimicrobials stewardship programs. InSeptember 2014, California Senate Bill 1311 was signed into law, furtherrequiring hospitals to adopt and implement an antimicrobial stewardshippolicy in accordance with guidelines established by federal governmentand professional organizations, and to establish a physician-supervisedmultidisciplinary antimicrobial stewardship committee with at least onephysician or pharmacist who has undergone specific training related tostewardship. In June 2016, the Centers for Medicare and Medicaid Systems(CMS) used proposed roles promoting antimicrobial stewardship inhospitals, with many industry experts expecting financial incentives tobe implemented in the coming two years. The present invention willfurther the government's and the healthcare industry's goals of betterantimicrobial stewardship.

Generalized steps of aspects of the present invention are shown inFIG. 1. Images in FIG. 1 show an aspect with distinct process steps:however, aspects of the present invention may be automated.

FIG. 2A to FIG. 2D show features of aspects of the present invention.FIG. 2A shows a detection sensitivity range for three representativepathogens. Dashed lines show zero-concentration signal levels. FIG. 2Bshows the “Crocodile” (Titertek-Berthold) automated fast-AST prototypeplatform which may be used in the present invention. FIG. 2C is aschematic showing anionic bacteria interacting with cationic nanolabelsand polymers. The decreased solubility of the resulting neutralcomplexes allows magnetic beads to bind. FIG. 2D shows data for S.aureus with a SensiTitre® Gram Positive panel (GPALL3F) showing abacteriostatic (clindamycin) and bactericidal (penicillin) antimicrobialresults relative to the high-growth and “frozen-in-time (FIT)” controls.

As is known to those skilled in the art, AST platforms may yield minimuminhibitory concentration (MIC) results and/or qualitative susceptibilityresults (QSRs) for each antimicrobial tested. MICs are commonly known tobe the lowest concentration of antimicrobial that inhibits microorganismgrowth and provides physicians with dosing information. QSRs may alsoprovide physicians with similar dosing information but may not provide anumerical MIC. AST assays are predominantly configured to test multipleantimicrobials in parallel for each obtained biological sample. In orderto produce MIC or QSR results, dilution series are required for eachantimicrobial. Thus, for liquid-based ASTs, termed “broth microdilution”by the CLSI, assays are commonly performed in cartridges and/ormicroplates, which enable parallel testing of different antimicrobialsat different concentrations.

Long times to obtain an AST determination result in incompleteinformation being delivered to physicians. These long times oftenprevent the identification of rates of antimicrobial efficacy, or killkinetics. This additional information may be important for informingtreatment. Current ASTs, which are not determined until over six hours(and generally over twelve hours) after treatment commences, often losethe ability to discern differences between the rate of antimicrobialefficacy: an antimicrobial that kills a microorganism instantly looksthe same after twelve hours as one that killed it within four hours.

Table 1 estimates the effects of different treatments on the number ofbacteria after a two-hour incubation. Assuming a thirty minute doublingtime, untreated controls should increase by sixteen-fold. Treatmentgroups with a “potent” antimicrobial (defined as one having efficacyagainst the bacteria, for example) above the MIC should result inminimal microorganism growth and, in the case of bactericidalantimicrobials, death of the microorganism. Thus, fewer bacteria areexpected than the starting concentration. Treatment groups with a“potent” antimicrobial below its MIC should result in microorganismgrowth equal to or lesser than the no-antimicrobial control. Slow-actingantimicrobials, defined in this case as those requiring more than twohours to kill the bacteria (e.g., as it the case for bacteriostaticantimicrobials) will produce a signal between the starting concentrationand the sixteen-fold increase.

TABLE 1 Potent No antimicrobial No Step antimicrobial at conc. Stepantimicrobial Starting bacteria 5 × 10⁵    5 × 10⁵   5 × 10⁵ 5 × 10⁵concentration Estimated 8 × 10⁶ ≤8 × 10⁶ <5 × 10⁵ 5 × 10⁵ to bacteria <8× 10⁶ concentration after 2 hours, with 30 min. doubling time

The starting concentration of bacteria of 5×10⁵ CFU/ml is given in theAmerican Society for Microbiology's “Manual of AntimicrobialSusceptibility Testing”© 2005, with Marie B. Coyle as the coordinatingeditor, for the broth micro dilution technique. Since each well containsapprox. 100 μL, there are approx. 5×10⁴ bacteria per well. Standardfluorescent dyes begin to be quantifiable at approx. 0.1 nMconcentrations, which correspond to approximately 1.2×10¹⁰ molecules.Thus, for a thirty minute doubling time bacteria to be visible after twohours, each individual bacterium would have to be labeled with 1.5×10⁴fluorescent molecules. Practical considerations, such as fluorescentbackground and non-specific binding, may increase this number by ordersof magnitude. In order to enable compatibility with standard opticaldetectors, it may thus be advantageous to use a chemical and/orbiochemical amplifier that produces a detectable signal at lowerconcentrations.

Without wishing to be bound by theory, the present invention is based inpart on the principle of broth micro dilution. A culture to be assessedis diluted, most preferably to 1-10×10⁵ CFU/ml, and introduced to wellscontaining different antimicrobials at different concentrations, suchthat MICs can be determined for an appropriate panel of antimicrobials.The plate is then introduced into an incubator at the appropriatetemperature, most preferably 31-37° C., and under appropriateconditions, most preferably aerobic, for growing bacteria. During thistime, the microorganism can grow.

The broth may be cation-adjusted Mueller Hinton broth and may containadditional supplements known by those skilled in the art to beadvantageous for microbial growth, such as lysed horse blood, and/or fordetermining antimicrobial efficacies, such as high sodium chlorideconcentrations. The microplates may be agitated during this growthperiod, which may be advantageous for dispersing nutrients and/or gasexchange and/or antimicrobials in each well and/or decreasing biofilmformation.

Within zero to eight hours of the AST onset (most preferably zero tofour hours), a known quantity of signaling agent is added to each well.Adding reagents (including signal generators) may be performed by anautomated instrument or a semi-automated instrument or may be performedmanually.

Signaling agents (which may be referred to as “sticky-amps”) comprise amoiety capable of binding to a microorganism (e.g., an antibody and/or alectin that bind to a microorganism surface, a charged moiety and/or afunctional moiety that non-specifically binds to the microorganismsurface) and a chemical moiety capable of providing a signal orcontributing to production of a signal (e.g., an enzymechemiluminophore, and lanthanide chelate). Exemplary enzymes includehorseradish peroxidase, alkaline phosphatase, acetyl cholinesterase,glucose oxidase, beta-D-galactosidase, beta-lactamase, and a combinationthereof.

As used herein, signal generator may include one or more chemicalmoieties (i.e., “signal generators”) conjugated to one or more“microorganism receptors.” Signal generators include, but are notlimited to, one or more catalysts (including enzymes, metal-oxidenanoparticles, organometallic catalysts, nanoparticles designed forsignal amplification (such as those described in the U.S. ProvisionalApplications to which the present application claims priority andincorporates by reference in their entireties), bacteriophagescomprising signal generating elements, fluorophores (including organicfluorophores, europium, or ruthenium(II), rhenium(I), palladium(II),platinum(II)-containing organometallics), and/or colorimetric dyes(including organic “stains”). Combinations of the above may be used,such as nanoparticles, dendrimers, and/or other nanoscale structureswith enzymes, fluorophores, and/or organometallic molecules.

The chemical moiety may be conjugated to a signaling agent beforecontacting the signaling agent to a microorganism, while the signalingagent is initially contacted to a microorganism, or after the signalingagent has contacted a microorganism.

When the signaling agents are added to AST dilutions containing amicroorganism, signaling agent receptors (e.g., moieties that can bindspecifically or non-specifically to a microorganism) associate withmicroorganism surfaces. Thus, the more intact microorganisms, forexample, there are in solution, the greater the number of signalingagents that will be associated with these bacteria. Consequently, thereis an inverse relationship between the number of intact bacteria and thenumber of signaling agents that are “free” in solution, as defined bythose not bound to intact bacteria. Note that free signaling agents maybe bound to soluble microbial components if, for example, microorganismslyse in response to antimicrobial treatment.

The number of signaling agents that associate with and/or intercalateinto microorganism surfaces is proportional to the microorganism surfacearea. Microorganism surface area is strongly associated with trulyresistant microorganisms. In particular, in the case of microorganismsthat swell or elongate in response to MIC- and sub-MIC concentrations ofantimicrobials (e.g., filament forming bacteria), metabolic and/orvolumetric identifications are known to give false susceptibilityprofiles for “rapid” AST time points, defined as those less than sixhours. To overcome this limitation, the present invention translatesmicroorganism surface area (rather than volume) into a measurablesignal, most preferably an optical signal. The present methods are ableto accurately determine microorganism resistance profiles in less thansix hours.

In order to separate signaling agents associated with and/orintercalated into microorganisms from free signaling agents, it may benecessary to perform one or more separation and/or competitive bindingsteps. Such steps include, but are not limited to, centrifugation (e.g.,with a g-force >500×g), filtration (e.g., via a filter having poressmaller than or equal to 0.45 microns, and preferably smaller than orequal to 0.2 microns), electrophoresis, and/or magnetic capture; suchsteps are well-known to those skilled in the art.

In order to promote signaling agent binding and/or reduce background, itmay further be advantageous, before adding signaling agents, to separatemicroorganisms from the liquid in which they were suspended duringincubation. Such separations may include but are not limited to,centrifugation, filtration, electrophoresis, and/or magnetic capture.

When these data are compared across treatment groups, microbialresistance profiles may be determined, using steps similar tocurrently-used AST determinations. Additionally, these data may enabledetermination of rates of antimicrobial efficacy, or kill kinetics.

Signaling agents may be added together with microorganisms and orantimicrobials, such that they are present for the entire AST incubationperiod. This total period may be up to twenty-four hours but ispreferably within eight hours and more preferably within five hours.Alternatively, signaling agents may be added to microorganisms andantimicrobial after a prescribed incubation period. This period may beup to twenty-four hours but is preferably within eight hours and morepreferably within four hours.

Signaling agents are designed to associate with and/or intercalate inmicroorganism surfaces, including walls and/or membranes. Signalingagents designed for association comprise binding moieties including, butare not limited to, one or more antibodies, lectins, other proteins,small molecules with one or more charged chemical groups, smallmolecules with one or more functional chemical groups, phages,glycoproteins, peptides, aptamers, charged small molecules, smallmolecules with fixed charges, charged polymers, charged polymers withfixed charges, hydrophobic small molecules, charged peptide, chargedpeptides with fixed charges, peptides with alternating hydrophilic andhydrophobic regions, and/or small molecule ligands, which may or may notbe organometallic complexes. Molecules designed for microorganismassociation are well-known to those skilled in the art. Signaling agentsmay remain bound to microorganisms and/or may be internalized, thus allassociations are included. Signaling agents designed for intercalationmay include, but are not limited to, small hydrophobic molecules,hydrophobic peptides, and/or peptides with alternating hydrophobic andhydrophilic regions. Molecules designed for microorganism intercalationare well-known to those skilled in the art. Signaling agents may furtherbe specific to one or more types of microorganisms. Signaling agents mayhave multiple receptors. These may enhance binding and/or enablesimultaneous binding to two or more microorganisms, which may furtherserve to “agglutinate” bacteria. Prior to or concurrently with theaddition of signaling agents it may be advantageous to adjust thesolution pH. This may be beneficial for enhancing charge-chargeinteractions between microorganisms and signaling agents. The anioniccharge of microorganisms may be increased by titrating the solution pHabove neutral (more basic). It may thus be beneficial to utilizemoieties with one or more fixed, cationic charges.

It is noteworthy that the signaling agent may specifically bind to amicroorganism (e.g., an antibody that specifically binds to amicroorganism species or a strain of microorganism) or mynon-specifically binds to a microorganism (e.g., by a generic covalentor non-covalent bond formation and another non-specific chemicalassociation known in the art).

It is preferred that signaling agents bind native microorganismsurfaces.

Alternately, chemicals and/or biochemicals which are capable ofassociating with signaling agents may be added to the liquid in whichthe microorganisms are suspended during growth, such that chemicalsand/or biochemicals are incorporated into microorganisms duringincubation. This may serve to enhance signaling agent association withmicroorganisms. In alternative embodiments, the signaling agentsthemselves may be present in the liquid in which the microorganisms aresuspended during incubation and may be incorporated into microorganismsduring growth.

Preferably the signaling agents comprise an amplifier signal generator,such that the signal from each intact microorganism may be amplifiedbeyond the number of signaling agents associated with eachmicroorganism. For example, the enzyme horseradish peroxidase (HRP) isknown to be able to amplify signals >1×10⁴-fold. Thus, if one hundredHRP molecules are bound to each microorganism surface, an amplificationof 10⁶ may be achieved. This may increase the speed with which ASTdeterminations may be made by enabling discrimination of microorganismconcentrations that cannot otherwise be differentiated. Use of Europiumformulations similarly provides signal amplification.

Alternatively, the signaling agents may comprise optical dye precursorsknown to those skilled in the art as “membrane dyes” that are designedto greatly increase fluorescence emission upon intercalation into ahydrophobic region, such as a cell membrane. Assays designed with thesesignaling agents may require microorganisms to be concentrated into asmaller volume, approaching a plane, to produce sufficient signals so asto be easily optically measured. Interfering species may require the useof near-IR fluorophores.

Potential separation techniques include, but are not limited to,filtering (e.g., via a filter having pores smaller than or equal to 0.45microns, preferably smaller than or equal to 0.2 microns),centrifugation (e.g., with a g-force >500×g), electrophoresis,dielectrophoresis, and magnetic capture. These techniques are employedto separate signaling agents associated with microorganisms, which arestuck in a filter, pelleted in a centrifuge, and/or separatedelectrophoretically and/or magnetically, from those free in solution.Free signaling agents pass through a filter (“filtrate”), remain insolution after centrifugation or magnetic separation (“supernatant”),and/or run separately electrophoretically. Centrifugation may bestandard, density gradient, or differential centrifugation. Magneticseparation may require the addition of one or more magnetic particlesspecifically targeted to associate with or bind to microorganisms. Thesemay be added prior to or concurrently with signaling agent addition.

Such separation techniques may also isolate microorganisms that changemorphology in response to an antimicrobial treatment and may confound adetermination. An example of such a microorganism is filamentousbacteria which initially elongate in response to antimicrobialtreatment. This growth regime is known to those skilled in the art.Isolating and excluding filamentous bacteria from an assay, using aherein-described separation technique, will increase the accuracy of theobtained results.

Microorganism separation may be enhanced through the association ofparticles with microorganism species. For example, in the case ofmagnetic separation, magnetic beads may associate with microorganisms(specifically or non-specifically). Moieties present on magnetic beadsurfaces may bind the same surface (or a biomolecule thereof) ofmicroorganisms as the singling agent or different surface (or abiomolecule thereof). The magnetic beads may have the same and/ordifferent moieties as the signaling agents. For example, if a signalingagent comprises an antibody that binds to E. coli, then a magnetic beadmay be functionalized with the same antibody. In other examples, thesignaling agent may include a motif that binds a microorganism and themagnetic bead is functionalized to non-specifically bind tomicroorganisms.

The one or more binding moieties associated with the magnetic beads maybe identical of different to the chemical moiety associated with or ofthe signaling agent.

The one or more binding moieties associated with the magnetic beads maybind the microorganisms prior to, simultaneously with, or subsequent tothe biding of the signaling agent with the microorganism.

The one or more binding moieties associated with the magnetic beads mayassociate with one or more polymers that precipitate microorganisms. Theone or more polymers that precipitate microorganisms may cationic. Theone or more polymers that precipitate microorganisms may bepoly(ethylene glycol).

Magnetic beads, as are known to those skilled in the art, may range insize from 20 nm to 20 microns.

After separation, one or more assays to determine the number ofsignaling agents remaining after microorganism separation and/or thenumber of signaling agents removed during microorganism separation(“free” signaling agents) may be performed. Performing an assay for freesignaling agents provides a signal inversely proportional tomicroorganism concentration. In this case signaling agents associatedwith microorganisms may be either bound to or internalized bymicroorganisms. Alternatively, an assay may be performed for signalingagents associated with microorganisms. In this case, unlessmicroorganisms are specifically lysed, only bound signaling agents willcontribute to the signal.

In order to maximize separation efficiency, i.e., minimize the number offree signaling agents remaining, one or more washing steps may beperformed. These may be continuous, as in the cases of filtering,magnetic capture, or electrophoresis, and/or discrete, as in the casesof centrifugation or magnetic capture.

In alternative embodiments, signaling agents may not require washing.This may be the case when “membrane dye” signaling agents are used.Molecules not intercalated into microorganism membranes havesignificantly lower optical activities than intercalated species, thuswashing may not be required.

One or more washes may be performed before signaling agents are added tothe microorganisms. These washes may, for example, remove interferingspecies present in the liquid in which the microorganisms were suspendedduring incubation.

In embodiments, no wash is performed.

Signal development may require the addition of a “development solution.”For signaling agents comprising catalysts, the development solution maycomprise one or more signal precursors that can be converted to anoptically and/or electrically active signaling molecule. For signalingagents comprising encapsulated molecules, such as within nanoparticles,the development solution may comprise one or more reagents to releasethe encapsulated species. At a specified time after addition of thedevelopment solution, a colorimetric and/or electrochemical signal ma)be measured. Such signals include, but are not limited to, absorbance,fluorescence, time-resolved fluorescence, chemiluminescence,electrochemiluminescence, amperometric, voltammetric, impedance, and/orimpedance spectroscopy. The data may then be compared to determine ASTsand MICs, similarly to current AST protocols.

In embodiments, determining signal levels includes measuring the signallevels associated with intact microorganisms. Alternately oradditionally, determining signal levels includes measuring the signallevels not associated with intact microorganisms.

These processes may be performed directly from cultures, sub-cultures,positive blood cultures, samples. Treatments to concentratemicroorganisms and/or remove potential interfering species may beperformed prior to AST or prior to signaling agent addition.

Signaling agents may also be used with plate-based methods for ASTdetermination, such as gradient diffusion. They may be addedsimultaneously upon microorganism addition to plates or following a setincubation period. Spatial information for the optical and/or electricalsignal is important in these cases. With this approach an assay forintact microorganism-bound signaling agents may be preferable in orderto retain spatial information. In this case, one or more wash steps maybe performed prior to the addition of the development solution in orderto remove free signaling agents.

In embodiments, no wash is performed.

Alternatively, signaling agents may be designed to be up-taken bybacteria, e.g., which may be achieved through the use of bacteriophages.In such methods, an assay for free signaling agents is performed.

Alternatively, a blot-transfer approach, such as is standard withnitrocellulose paper, may be used to transfer bacteria or free signalingagents and a spatial assay then performed on the blotted paper.

Separation step(s) may not be required if the signaling agent produces asignal upon binding. Alternatively, a separation step-free process maybe achieved if the signaling agent becomes susceptible or resistant to aspecific developer solution constituent upon binding.

Final MIC and/or QSR output data may be interpreted by a user directlyfrom the data produced by the assays described herein. Alternatively,these data may be processed by one or more algorithms to yield MICsand/or QSRs. Reported MIC and/or QSR values may be derived from one ormore of the assays described herein or may be derived from one or moreof the assays described herein together with one or more known assaysfor microorganism growth including, but not limited to, metabolic dyeindicator assays, pH indicator assays, nucleic acid assays, and ATPassays.

Methods of the Present Invention

An aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in thepresence of an antimicrobial and a signaling agent under conditions thatpromote growth of the microorganisms, wherein the signaling agent iscapable of binding to a surface of the microorganisms; separating themicroorganisms bound by the signaling agent from the unbound signalingagent; and determining signal levels associated with the microorganismsas compared to one or more controls, thereby determining theantimicrobial susceptibility of the microorganisms.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in thepresence of an antimicrobial under conditions that promote growth of themicroorganisms; adding a signaling agent capable of binding to a surfaceof the microorganisms; separating the microorganisms bound by thesignaling agent from the unbound signaling agent; and determining signallevels associated with the microorganisms as compared to one or morecontrols, thereby determining the antimicrobial susceptibility of themicroorganisms. In embodiments, adding the signaling agent occurs priorto or during the incubating step or adding the signaling agent occursafter the incubating step.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includessteps of incubating a liquid suspension of microorganisms in a cartridgecomprising a plurality of chambers, each chamber containing one or moreantimicrobials, under conditions that promote growth of themicroorganisms; adding a signaling agent to the plurality of chambers,wherein the signaling agent is capable of binding to a surface of themicroorganisms; removing unbound signaling agent; and determiningsignaling levels in the plurality of chambers as compared to one or morecontrols, thereby determining the susceptibility of microorganisms tothe one or more antimicrobials. In embodiments, the cartridge furtherincludes one or more control chambers (e.g., at least 2, 4, 6, 8, 12,24, 48, 96, 192, 384, 1536 or more chambers) that do not containantimicrobials or one or more antimicrobials for which themicroorganisms are not susceptible.

In embodiments of an above aspect, binding to a surface of themicroorganisms is non-specific, e.g., comprising a non-covalentinteraction and via forming a covalent bond.

In embodiments of an above aspect, the signaling agent may include achemical and/or biochemical group capable of binding a surface of themicroorganisms, wherein the surface comprises one or more of membranes,walls, proteins, organelles, saccharides, lipids, cell envelope, and/ornucleic acids.

In embodiments of an above aspect, the signaling agent may include achemical and/or biochemical group capable of binding a biomolecule ofthe surface of the microorganisms, wherein the surface biomolecule isselected from peptidoglycans, mureins, mannoproteins, porins,beta-glucans, chitin, glycoproteins, polysaccharides,lipopolysaccharides, lipooligosaccharides, lipoproteins, endotoxins,lipoteichoic acids, teichoic acids, lipid A, carbohydrate bindingdomains, efflux pumps, other cell-wall and/or cell-membrane associatedproteins, other anionic phospholipids, and a combination thereof.

In embodiments of an above aspect, the signaling agent may include asignal amplifier and one or more chemical moieties capable of bindingnon-specifically to a surface of the microorganisms.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includesincubating microorganisms in the presence of an antimicrobial and asignaling agent under conditions that promote growth of themicroorganisms, wherein the signaling agent comprises a signal amplifierand one or more chemical moieties capable of binding non-specifically toa surface of the microorganisms; separating the microorganisms bound bythe signaling agent from the unbound signaling agent; and determiningsignal levels associated with the microorganisms as compared to one ormore controls, thereby determining the antimicrobial susceptibility ofthe microorganisms.

Another aspect of the present invention is a method for determiningantimicrobial susceptibility of microorganisms. The method includesincubating microorganisms in the presence of an antimicrobial underconditions that promote growth of the microorganisms; adding a signalingagent comprising a signal amplifier and one or more chemical moietiescapable of binding non-specifically to a surface of the microorganisms;separating the microorganisms bound by the signaling agent from theunbound signaling agent; and determining signal levels associated withthe microorganisms as compared to one or more controls, therebydetermining the antimicrobial susceptibility of the microorganisms. Inembodiments, the signaling agent occurs prior to, at the beginning of,or during the incubating step, preferably during the incubating step. Inembodiments, the microorganisms are incubated in a liquid suspension.

In embodiments of an above aspect, the liquid suspension may be preparedby inoculating a liquid media with a microbial isolate grown from abiological sample.

In embodiments of an above aspect, the liquid suspension ofmicroorganisms may be prepared from an unprocessed biological sample,e.g., an unprocessed biological sample has not undergone a culturingstep.

In embodiments of an above aspect, the liquid suspension ofmicroorganisms may be prepared from a cultured or processed biologicalsample.

In embodiments of an above aspect, the biological sample is selectedfrom blood, cerebrospinal fluid, urine, stool, vaginal, sputum,bronchoalveolar lavage, throat, nasal/wound swabs, and a combinationthereof.

In embodiments of an above aspect, the method does not involve a step ofcapturing microorganisms on a solid surface prior to or duringincubation.

In embodiments of an above aspect, the method does not include a step ofgrowing microorganisms on a solid surface during or subsequent to theincubating step.

In embodiments of an above aspect, the incubating may include agitatingthe liquid suspension of microorganisms.

In embodiments of an above aspect, the liquid suspension ofmicroorganisms may be agitated by means of mechanical, acoustic, and/ormagnetic agitation continuously or discretely during the incubating.

In embodiments of an above aspect, the incubating occurs at 31-37° C.Comparison of the present invention to currently-used AST systems

The present invention is superior to currently-used AST methods, in partbecause it provides accurate AST results in significantly less time.

Three automated AST systems that are currently used in clinics areBioMeriéux's Vitek2, Beckman Dickinson's Phoenix, and Beckman-Coulter'sMicroScan. A comparison between steps in currently-used AST systems andthe present invention are shown in FIG. 3.

The processes described in this invention may be performed in at leasttwo modes. The first is for standard isolates, with no changes tocurrent laboratory workflows. The second is direct from positive bloodcultures.

For standard isolate processing, the present invention is compatiblewith existing clinical laboratory workflows and, thus, requires nochanges. As shown in “step 8” of FIG. 3, current susceptibility (AST)testing is performed after colony isolation (step 6) and microorganismconcentration standardization (step 7). In this workflow, the presentinvention would replace current systems at “step 8.” Because AST resultswith the present invention are available within a healthcare worker'sthe shift (<5 hours), utility may increase the speed with which patientsreceive optimized therapies (step 9) by up to one day in practice.Automation may be designed to include “step 7” and, potentially,additional steps in the workflow. Such automation is known to thoseskilled in the art. Note that FIG. 3 illustrates the workflow for bloodsamples. Many sample types, such as urine and swabs, may be streakeddirectly on plates (step 4). In this case, the gram stain may beperformed at step 6.

For a blood test, the currently-used AST systems require an obtainedblood culture to become detectibly positive (which takes ten or morehours), followed by a sub-culture step (of at least twelve hours), andthen an AST test (which requires a minimum of eight hours): this totalsover forty-eight hours, depending on the pathogen, and often takesgreater than three days in practice. In most workflows, theidentification of the organism happens after the sub-culture step andincreasingly done by mass spectrometry. Since both identification andAST results are required for clinicians or pharmacists to prescribeproper targeted antimicrobials, this delay to AST results directlyextends the duration of broad-spectrum antimicrobial treatment.Furthermore, the wait is often compounded by one-shift operation commonin many clinical microbiology laboratories.

Alternatively, the present invention may be used directly from positiveblood cultures. After the standard step 1 and step 2 of blood draw andincubation/culture, if the culture is positive, the culture bottle wouldmove directly to a microorganism isolation (step 3) and then into anautomated system (step 4). The present invention can be fully automated,requiring a technician to only load the system with a standard cartridgewith microorganism dilutions and then initiate the four-hour “fast-AST”process. The lab technician would then receive the same standardphenotypic results for AST of a minimum inhibitory concentration(“MIC”). However, the streamlined process would reduce the time to ASTby over twenty-four hours in theory, and potentially two days inpractice, and simplify lab workflow.

The currently used AST systems perform variants of the ClinicalLaboratory Standards Institute (CLSI) broth microdilution procedure.Bacteria are inoculated into multiple wells in parallel, each of whichcontains one (or more) antimicrobials at a known concentration and anutrient broth. Wells are inoculated at 5×10⁵ CFU/ml to ensure bacteriaare in the log growth phase, important for detecting accurate responsesto antimicrobials. Microorganism detection is then performed visually.

The slow speed of phenotypic AST testing is due, in part, to itsreliance on microorganism growth in order to produce a detectableoptical signal. Bacteria cannot be quantified by optical densitymeasurements below a concentration of ˜1×10⁸ CFU/ml, rendering the CLSIstarting concentration invisible for a minimum of eight doubling times.Since differentiation of microorganism growth in the slowest-growingwell from the no-growth well is critical for minimum inhibitoryconcentration (MIC) determinations, significantly longer times arerequired. As is known to those skilled in the art, some existingplatforms overcome these growth issues by including metabolic probes inthe liquid in which the microorganisms are suspended during incubation.However, inclusion of these probes may miss growth regimes, such asfilamentous growth, and may impact the accuracy of results.

Once the AST-specific steps have commenced, the currently-used ASTsystems still typically require over eight hours to report results forsimple, highly-susceptible bacteria and require over ten hours forpathogens with complex resistance profiles or slow growth kinetics, seeFIG. 4.

Additionally, the currently-used automated AST systems suffer from twoshortcomings that prevent the reporting of accurate results in less thansix hours: 1) very major errors, inaccurate “susceptible” calls fortruly-resistant strains; and 2) major errors, inaccurate “resistant”calls for truly-susceptible strains. Indeed, these issues have requiredBioMeriéux and BD to revise their initial four-hour speed claims for theVitek2® and Phoenix®.

The existence of very major errors is explained in part by the metabolicenergy expended by the microorganisms in achieving antimicrobialresistance. Resistant microorganisms may alter energy expenditures inresponse to antimicrobials, confounding the results of metabolic probesaround the MIC. These may also result from the present of additives,such as redox indicators, in the growth media. The prevalence of majorerrors is due primarily to filamentous growth of certain bacteria. Thisgrowth regime is a common antimicrobial response amongst gram-negativebacteria, in particular to cell-wall-acting antimicrobials, such asβ-lactams. Filamentous bacteria continue to replicate their internalcontents but do not septate. Thus, again, metabolic probes giveerroneous near-MIC results. The removal of filamentous bacteria wasshown to significantly reduce major errors for the AST method.

Measurements of relative microorganism surface area, as used in thepresent invention, overcome the pitfalls of metabolic probes for AST.First, since relative surface area is not confounded by shifts inmetabolic activity, fast-AST enables rapid, accurate resistance calls.Second, surface area measurements prevent over-resistance calls. Incontrast to volumetric measurements obtained with metabolic probes ofthe currently-used AST systems, surface area measurements enableaccurate differentiation between true resistance and filamentous growth.As illustrated in the schematic of FIG. 39, volumes of resistant andsusceptible filamentous bacteria are difficult to distinguish. But thelack of septation creates a filamentous surface area significantly lowerthan that of truly resistant bacteria. Thus, by amplifying eachbacteria's surface area, the present invention is able to accuratelycall four-hour, β-lactam (ampicillin) MICs for E. coli samples (see, thebelow Examples). As illustrated in FIG. 39, the surface areadifferential between elongation and “true” resistance approaches ⅔,which may be detected with an amplified signal.

Patient

As used herein, the term “patient” (also interchangeably referred to as“host” or “subject”) refers to any host that can serve as a source ofone or more of the biological samples or specimens as discussed herein.In certain aspects, the donor will be a vertebrate animal, which isintended to denote any animal species (and preferably, a mammalianspecies such as a human being). In certain embodiments, a “patient”refers to any animal host, including but not limited to, human andnon-human primates, avians, reptiles, amphibians, bovines, canines,caprines, cavities, corvines, epines, equines, felines, hircines,lapines, leporines, lupines, ovines, porcines, racines, vulpines, andthe like, including, without limitation, domesticated livestock, herdingor migratory animals or birds, exotics or zoological specimens, as wellas companion animals, pets, and any animal under the care of aveterinary practitioner.

Biological Samples

The biological sample is any sample that contains a microorganism, e.g.,a bacterium and a fungal cell.

Exemplary biological samples include, but are not limited to, wholeblood, plasma, serum, sputum, urine, stool, white blood cells, red bloodcells, buffy coat, tears, mucus, saliva, semen, vaginal fluids,lymphatic fluid, amniotic fluid, spinal or cerebrospinal fluid,peritoneal effusions, pleural effusions, exudates, punctates, epithelialsmears, biopsies, bone marrow samples, fluids from cysts or abscesses,synovial fluid, vitreous or aqueous humor, eye washes or aspirates,bronchoalveolar lavage, bronchial lavage, or pulmonary lavage, lungaspirates, and organs and tissues, including but not limited to, liver,spleen, kidney, lung, intestine, brain, heart, muscle, pancreas, and thelike, swabs (including, without limitation, wound swabs, buccal swabs,throat swabs, vaginal swabs, urethral swabs, cervical swabs, rectalswabs, lesion swabs, abscess swabs, nasopharyngeal swabs, and the like),and any combination thereof. Also included are bacteria cultures orbacteria isolates, fungal cultures or fungal isolates. Theordinary-skilled artisan will also appreciate that isolates, extracts,or materials obtained from any of the above exemplary biological samplesare also within the scope of the invention.

Microorganisms obtained from a biological sample may be cultured orotherwise processed as is routinely performed in the art.

Exemplary Microorganisms

As used herein, infection is meant to include any infectious agent of amicrobial origin, e.g., a bacterium, a fungal cell, an archaeon, and aprotozoan. In preferred examples, the infectious agent is a bacterium.e.g., a gram-positive bacterium, a gram-negative bacterium, and anatypical bacteria. The term “antimicrobial resistant microorganism” is amicroorganism (e.g., bacterium, fungus, archeaon, and protozoan) that isresistant to one or more distinct antimicrobials, i.e., anti-bacterialdrugs, antifungal drugs, anti-archaea medications, and anti-protozoandrugs.

The microorganisms (e.g., a liquid suspension of microorganisms) mayinclude one strain of microorganism. The microorganisms may include onespecies of microorganism. The microorganisms may include more than onestrain of microorganism. The microorganisms may include one order ofmicroorganism. The microorganisms may include one class ofmicroorganism. The microorganisms may include one family ofmicroorganism. The microorganisms may include one kingdom ofmicroorganism.

The microorganisms (e.g., a liquid suspension of microorganisms) mayinclude more than one strain of microorganism. The microorganisms mayinclude more than one species of microorganism. The microorganisms mayinclude more than one genus of microorganism. The microorganisms mayinclude more than one order of microorganism. The microorganisms mayinclude more than one class of microorganism. The microorganisms mayinclude more than one family of microorganism. The microorganisms mayinclude more than one kingdom of microorganism.

The microorganism may be a bacterium. Examples of bacterium include andare not limited to Acetobacter aurantius, Acinetobacter bitumen.Acinetobacter spp., Actinomyces israelii., Actinomyces spp., Aerococcusspp., Agrobacterium radiobacter, Agrobacterium tumefaciens, Anaplasma.Anaplasma phagocytophilum, Azorhizobium caulinodans. Azotobactervinelandii, Bacillus, Bacillus anthracis, Bacillus brevis, Bacilluscereus, Bacillus fusiformis, Bacillus licheniformis, Bacillusmegaterium, Bacillus mycoides, Bacillus spp., Bacillusstearothermophilus. Bacillus subtilis. Bacillus Thuringiensis.Bacteroides. Bacteroides fragilis, Bacteroides gingivalis. Bacteroidesmelaninogenicus (also known as Prevotella melaninogenica), Bartonella.Bartonella henselae, Bartonella quintana. Bartonella spp., Bordetella.Bordetella bronchiseptica. Bordetella pertussis, Bordetella spp.,Borrelia burgdorferi. Brucella. Brucella abortus. Brucella melitensis.Brucella spp., Brucella suis, Burkholderia. Burkholderia cepacia.Burkholderia mallei. Burkholderia pseudomallei, Calymmatobacteriumgranulomatis. Campylobacter. Campylobacter coli. Campylobacter fetus.Campylobacter jejuni. Campylobacter pylori. Campylobacter spp.,Chlamydia. Chlamydia spp., Chlamydia trachomatis. Chlamydophila,Chlamydophila pneumoniae (previously called Chlamydia pneumoniae),Chlamydophila psittaci (previously called Chlamydia psittaci).Chlamydophila spp., Clostridium, Clostridium botulinum, Clostridiumdifficile, Clostridium perfringens (previously called Clostridiumwelchii). Clostridium spp., Clostridium tetani, Corynebacterium,Corynebacterium diphtheriae, Corynebacterium fusiforme, Corynebacteriumspp., Coxiella burnetii, Ehrlichia chaffeensis, Ehrlichia spp.,Enterobacter cloacae, Enterobacter spp., Enterococcus, Enterococcusavium, Enterococcus durans, Enterococcus faecalis. Enterococcus faecium.Enterococcus galllinarum, Enterococcus maloratus, Enterococcus spp.,Escherichia coli, Francisella spp., Francisella tularensis,Fusobacterium nucleatum. Gardenerella spp., Gardnerella vaginalis.Haemophilius spp., Haemophilus, Haemophilus ducreyi, Haemophilusinfluenzae. Haemophilus parainfluenzae. Haemophilus pertussis.Haemophilus vaginalis. Helicobacter pylori. Helicobacter spp.,Klebsiella pneumoniae, Klebsiella spp., Lactobacillus. Lactobacillusacidophilus, Lactobacillus bulgaricus, Lactobacillus casei,Lactobacillus spp., Lactococcus lactis. Legionella pneumophila.Legionella spp., Leptospira spp., Listeria monocytogenes. Listeria spp.,Methanobacterium extroquens. Microbacterium multiforme. Micrococcusluteus. Moraxella catarrhalis. Mycobacterium. Microbacterium avium.Mycobacterium bovis, Mycobacterium diphtheriae, Mycobacteriumintracellulare, Mycobacterium leprae. Mycobacterium lepraemurium.Mycobacterium phlei. Mycobacterium smegmatis, Mycobacterium spp.,Mycobacterium tuberculosis, Mycoplasma, Mycoplasma fermentans.Mycoplasma genitalium, Mycoplasma hominis, Mycoplasma penetrans,Mycoplasma pneumoniae. Mycoplasma spp., Neisseria, Neisseriagonorrhoeae, Neisseria meningitidis. Neisseria spp., Nocardia spp.,Pasteurella, Pasteurella multocida, Pasteurella spp., Pasteurellatularensis. Peptostreptococcus. Porphyromonas gingivalis. Prevotellamelaninogenica (previously called Bacteroides melaninogenicus), Proteusspp., Pseudomonas aeruginosa. Pseudomonas spp., Rhizobium radiobacter.Rickettsia. Rickettsia prowazekii, Rickettsia psittaci, Rickettsiaquintana. Rickettsia rickettsii. Rickettsia spp., Rickettsia trachomae,Rochalimaea, Rochalimaea henselae, Rochalimaea quintana. Rothiadentocariosa, Salmonella. Salmonella enteritidis, Salmonella spp.,Salmonella typhi. Salmonella typhimurium. Serratia marcescens. Shigelladysenteriae. Shigella spp., Spirillum volutans. Staphylococcus.Staphylococcus aureus. Staphylococcus epidermidis. Staphylococcus spp.,Stenotrophomonas maltophilia, Stenotrophomonas spp., Streptococcus,Streptococcus agalactiae, Streptococcus avium. Streptococcus bovis,Streptococcus cricetus, Streptococcus facetum. Streptococcus faecalis,Streptococcus mitis. Streptococcus gallinarum. Streptococcus lactis.Streptococcus mitior, Streptococcus mitis, Streptococcus mutans.Streptococcus oralis. Streptococcus pneumoniae. Streptococcus pyogenes.Streptococcus rattus, Streptococcus salivarius, Streptococcus sanguis.Streptococcus sobrinus, Streptococcus spp., Treponema. Treponemadenticola, Treponema pallidum, Treponema spp., Ureaplasma spp., Vibrio,Vibrio cholerae, Vibrio comma, Vibrio parahaemolyticus. Vibrio spp.,Vibrio vulnificus, viridans streptococci. Wolbachia. Yersinia. Yersiniaenterocolitica, Yersinia pestis. Yersinia pseudotuberculosis., andYersinia spp.

The microorganism may be a fungus. Examples of fungi include and are notlimited to Aspergillus spp., Blastomyces spp., Candida spp.,Cladosporium. Coccidioides spp., Cryptococcus spp., Exserohilum,fusarium. Histoplasma spp., Issatchenkia spp., mucormycetes.Pneumocystis spp., ringworm scedosporium. Sporothrix, and Stachybotrysspp.

The microorganism may be a protozoan. Examples of protozoan include andare not limited to Entamoeba histolytica. Plasmodium spp., Giardialamblia, and Trypanosoma brucei.

Exemplary Antimicrobials

When the microorganism is a bacterium, exemplary antimicrobials includeAmikacin. Aminoglycoside, Aminoglycoside amoxicillin, Aminoglycosides,Amoxicillin, Amoxicillin/clavulanate. Ampicillin, Ampicillin/sulbactam,Antitoxin. Arsphenamine. Azithromvcin. Azlocillin, Aztreonam, β-lactam,Bacitracin, Capreomycin, Carbapenems, Carbenicillin, Cefaclor,Cefadroxil, Cefalexin, Cefalothin, Cefalotin, Cefamandole, Cefazolin,Cefdinir, Cefditoren, Cefepime, Cefixime, Cefoperazone, Cefotaxime,Cefoxitin, Cefpodoxime, Cefprozil, Ceflaroline, Ceftaroline fosamil,Ceftazidime, Ceftibuten, Ceftizoxime. Ceftobiprole, Ceftriaxone,Cefuroxime, Cephalosporin, Chloramphenicol, Chloramphenicol(Bs),Ciprofloxacin, Clarithromycin, Clindamycin, Clofazimine, Cloxacillin,Colistin, Co-trimoxazole, Cycloserine, Dalbavancin, Dapsone, Daptomycin,Demeclocycline, Dicloxacillin. Dirithromycin, Doripenem. Doxycycline.Enoxacin, Ertapenem. Erythromycin, Ethambutol, Ethambutol(Bs),Ethionamide, Flucloxacillin, Fluoroquinolone, Fluoroquinolones,Fosfomycin, Furazolidone, Fusidic acid, Gatifloxacin, Geldanamycin.Gemifloxacin, Gentamicin, Grepafloxacin, Herbimycin,Imipenem/Cilastatin, Isoniazid, Kanamycin, Levofloxacin, Lincomycin,Linezolid, Lomefloxacin, Loracarbef, Macrolides, Mafenide, Meropenem,Methicillin, Metronidazole, Mezlocillin, Minocycline, Moxifloxacin,Mupirocin, Nafcillin, Nafcillin, Nalidixic acid, Neomycin, Netilmicin,Nitrofurantoin(Bs), Norfloxacin, Ofloxacin, Oritavancin, Oxacillin,Oxvtetracycline, Paromomycin, Penicillin, Penicillin G, Penicillin V,Piperacillin, Piperacillin/tazobactam, Platensimycin, Polymyxin B,Posizolid, Pyrazinamide, Quinupristin/Dalfopristin. Radezolid,Raxibacumab. Rifabutin, Rifampicin, Rifampin, Rifapentine, RifaximinRoxithromycin, Silver sulfadiazine, Sparfloxacin, Spectinomvcin,Spectinomycin(Bs), Spiramycin, Streptogramins, Streptomycin, Sulbactam,Sulfacetamide, Sulfadiazine, Sulfadimethoxine, Sulfamethizole,Sulfamethoxazole, Sulfanilimide, Sulfasalazine, Sulfisoxazole,Sulfonamidochrysoidine, Tedizolid, Teicoplanin, Teixobactin, Telavancin,Telithromycin, Temafloxacin, Temocillin, Tetracycline, Thiamphenicol,ticarcillin, Ticarcillin/clavulanate, Ticarcillin/clavulanic acid,Tigecycline. Tigecycline(Bs), Tinidazole, TMP/SMX, Tobramycin,Torezolid, Trimethoprim(Bs), Trimethoprim-Sulfamethoxazole,Troleandomycin, Trovafloxacin, Vancomycin, and generics thereof or avariant thereof.

Antimicrobials whose interactions with the microorganism affect and areaffected by the negative charges on the microorganism surface include:polycationic aminoglycosides, which upon binding the cell surfacedisplace Mg²⁺ ions, which bridge lipid membrane components, therebydisrupting the outer membrane and enhancing drug uptake; cationicpolymyxins (colistin and polymyxin B), whose binding to themicroorganism cell is also dependent on the membrane's negative chargeand for which both mutational and plasmid-mediated resistance occurs byreducing membrane negative charge; and daptomycin, a lipopeptide thatresembles host innate immune response cationic antimicrobial peptidesand requires Ca²⁺ and phosphatidyl glycerol for its membrane-disruptingmechanism of action and for which resistance can also involve alterationin cell surface charge.

When the microorganism is a fungus, exemplary antimicrobials include5-fluorocytosine, Abafungin, Albaconazole. Allylamines, Amphotericin B,Ancobon, Anidulafungin, Azole, Balsam of Peru, Benzoic acid, Bifonazole,Butoconazole, Candicidin, Caspofungin, Ciclopirox, Clotrimazole,Cresemba, Crystal violet, Diflucan, Echinocandins, Econazole,Efinaconazole, Epoxiconazole, Fenticonazole, Filipin, Fluconazole,Flucytosine, Grifulvin V, Griseofulvin, Gris-Peg, Haloprogin. Hamycin,Imidazoles, Isavuconazole, isavuconazonium, Isoconazole, Itraconazole,Ketoconazole, Lamisil, Luliconazole, Micafungin, Miconazole, Natamycin,Noxafil, Nystatin, Omoconazole, Onmel, Oravig, Oxiconazole,Posaconazole, Propiconazole, Ravuconazole, Rimocidin. Sertaconazole,Sporanox, Sulconazole. Terbinafine, Terconazole, Thiazoles,Thiocarbamate antifungal, Tioconazole, Tolnaftate, Triazoles,Undecylenic acid, Vfend, Voriconazole, and generics thereof or a variantthereof.

When the microorganism is a protozoan, exemplary antimicrobials include8-Aminoquinoline, Acetarsol, Agents against amoebozoa, Ailanthone,Amodiaquine, Amphotericin B, Amprolium. Antitrichomonal agent,Aplasmomycin. Arsthinol, Artelinic acid, Artemether,Artemether/lumefantrine, Artemisinin, Artemotil, Arterolane, Artesunate,Artesunate/amodiaquine, Atovaquone. Atovaquone/proguanil, Azanidazole,Azithromycin, Benznidazole, Broxyquinoline, Buparvaquone, Carbarsone,Camidazole, Chiniofon, Chloroquine, Chlorproguanil,Chlorproguanil/dapsone, Chlorproguanilidapsone/artesunate,Chlorquinaldol, Chromalveolate antiparasitics, Cinchona, Cipargamin,Clazuril, Clefamide, Clioquinol. Coccidiostat, Codinaeopsin, Cotrifazid,Cryptolepine. Cycloguanil, Dehydroemetine, Difetarsone,Dihydroartemisinin, Diloxanide, Diminazen. Disulfiram, Doxycycline,Eflornithine, ELQ-300, Emetine. Etofamide, Excavata antiparasitics,Fumagillin, Furazolidone, Glycobiarsol, GNF6702, Halofantrine,Hydroxychloroquine, Imidocarb, Ipronidazole. Jesuit's bark, KAF156,Lumefantrine. Maduramicin, Mefloquine. Megazol, Meglumine antimoniate,Melarsoprol, Mepacrine. Metronidazole, Miltefosine, Neurolenin B,Nicarbazin, Nifurtimox, Nimorazole, Nitarsone, Nitidine, Nitrofural,Olivacine, Ornidazole, Oroidin, Pamaquine. Paromomycin, Pentamidine,Pentavalent antimonial, Phanquinone, Phenamidine, Piperaquine,Primaquine, Proguanil. Project 523, Propenidazole, Pyrimethamine,Pyronaridine, Quinfamide, Quinine, Ronidazole, Schedula Romana,SCYX-7158, Secnidazole, Semapimod, Sodium stibogluconate, Spiroindolone,Sulfadoxine, Sulfadoxine-Pyrimethamine, Sulfalene. Suramin, Tafenoquine,Teclozan, Tenonitrozole, Tilbroquinol, Tinidazole. Trimetrexate,Trypanocidal agent, Warburg's tincture, and generics thereof or avariant thereof.

An antimicrobial may be a drug that operates by a mechanism similar to aherein-recited drug.

Other antimicrobial drugs known in the art may be used in the presentinvention.

Liquid Suspensions

A liquid suspension of microorganisms may by agitated using mechanical,acoustic, and/or magnetic agitation. Examples of mechanical agitationinclude shaking or rocking and/or use of stir bars, stir paddles, stirblades, and/or stir propellers or impellers.

The microorganism separation is performed by centrifugation (e.g., witha g-force >500×g), magnetic separation, filtration (e.g., via a filterhaving pores smaller than or equal to 0.45 microns, and preferablysmaller than or equal to 0.2 microns), electrophoresis,dielectrophoresis, precipitation, agglutination, or any combinationthereof.

The liquid may include a growth media, such as cation-adjusted MuellerHinton broth. This media may contain one or more additives, known tothose skilled in the art to promote microorganism growth, and stability.In addition to different antimicrobials, different test wells maycontain one or more additives known to improve AST accuracy for specificantimicrobials. For example, additional sodium chloride may be added totests comprising oxacillin and additional calcium may be added to testscomprising daptomycin.

Cartridges

The type of cartridge is not limited. A cartridge is a container that iscapable of holding and allowing growth of a liquid suspension ofmicroorganisms. Non-limited examples of a cartridge include a cultureflask, a culture dish, a petri dish, a bioassay dish, a culture tube, atest tube, a microfuge tube, a bottle, a microwell plate, a multiwellplate, a microtiter plate, a microplate. The cartridge may contain onechamber. The cartridge may include a plurality of chambers each chamberbeing a space capable of holding a liquid suspension in physicalisolation from another space; an example of a chamber is a well in amultiwall plate. The cartridge may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 24, 48, 96, 192, 384, 1536, or more chambers, and any numberof chambers in between.

Optical Device

Any optical device (e.g., microscope, microplate reader) with a numberof varying features is capable of detecting a signal is useful in thepresent invention. For instance: broad spectrum lamp (e.g., xenon),narrow spectrum lamps, laser, LED, multi-photon, confocal ortotal-internal reflection illumination can be used for excitation.Cameras (single or multiple), single or arrays (1D or 2D) ofphotodiodes, avalanche photodiodes, CMOS or CCD sensors, solid-statephotomultipliers (e.g. silicon photomultipliers), and/or Photomultipliertube (single or multiple) with either filter-based or grating-basedspectral resolution (one or more spectrally resolved emissionwavelengths) are possible on the detection side.

Kits

The terms “kits” and “systems,” as used herein in the present invention,are intended to refer to such things as combinations of multiplesignaling agents with one or more other types of elements or components(e.g., other types of biochemical reagents, signal detection reagents,controls (i.e., positive and negative controls, e.g., chemicallysensitive/resistant microorganisms), separation means (e.g., filters andmagnetic beads), containers, packages such as packaging intended forcommercial sale, substrates/cartridges to which microorganismsuspensions can be cultured, processed, or contained, electronichardware components, and software recorded on a non-transitoryprocessor-readable medium).

Another aspect of the present invention is a kit for determiningantimicrobial susceptibility of microorganisms. The kit includes asignaling agent capable of binding to a surface of the intactmicroorganisms of interest; a solution for incubating a samplecontaining microorganisms; and one or more reagents for generatingsignals from the signaling agent.

In embodiments, the signaling agent is associated with one or morebinding moieties capable of binding directly or indirectly to the intactmicroorganisms of interest.

In embodiments, the one or more binding moieties are selected fromantibodies, lectins, natural and/or synthetic peptides, synthetic and/ornatural ligands, synthetic and/or natural polymers, synthetic and/ornatural glycopolymers, carbohydrade-binding proteins and/or polymers,glycoprotein-binding proteins and/or polymers, charged small molecules,other proteins, bacteriophages, and/or aptamers.

In embodiments, the one or more binding moieties may be a polyclonaland/or monoclonal antibody.

In embodiments, the one or more binding moieties may be a syntheticand/or natural ligand and/or peptide. The ligand and/or peptide may beselected from bis(zinc-dipicolylamine). TAT peptide, serine proteases,cathelicidins, cationic dextrins, cationic cyclodextrins, salicylicacid, lysine, and a combinations thereof.

In embodiments, the one or more binding moieties may be a syntheticand/or natural polymer and/or glycopolymer. The natural and/or syntheticpolymer may be amylopectin,Poly(N-[3-(dimethylamino)propyl]methacrylamide), poly(ethyleneimine),poly-L-lysine, poly[2-(N,N-dimethylamino)ethyl methacrylate], andcombinations thereof. The natural and/or synthetic polymer and/orglycopolymer my include moieties including, but not limited to,chitosan, gelatin, dextran, trehalose, cellulose, mannose, cationicdextrans and cyclodextrans, or combinations thereof including, but notlimited to, co-block, graft, and alternating polymers.

In embodiments, the one or more binding moieties may include aglycoprotein selected from mannose-binding lectin, other lectins,annexins, and combinations thereof.

In embodiments, the one or more binding moieties may include two or morebinding moieties.

In embodiments, the one or more binding moieties may bind directly orindirectly to one or more biomolecules present on the microorganismsurface. Exemplary biomolecules include peptidoglycans, mureins,mannoproteins, porins, beta-glucans, chitin, glycoproteins,polysaccharides, lipopolysaccharides, lipooligosaccharides,lipoproteins, endotoxins, lipoteichoic acids, teichoic acids, lipid A,carbohydrade binding domains, efflux pumps, other cell-wall and/orcell-membrane associated proteins, other anionic phospholipids, and acombination thereof.

In embodiments, the binding moiety is a nanoparticle.

In embodiments, the binding moiety is a bacteriophage.

In embodiments, the one or more binding moieties may bind to one or morebiomolecules specifically.

In embodiments, the one or more binding moieties may bind to one or morespecies-specific biomolecules.

In embodiments, the one or more binding moieties may bind to themicroorganisms non-specifically, e.g., via a non-covalent interactionand via forming a covalent bond.

In embodiments, the kit further includes magnetic beads to magneticallyseparate the microorganisms from the supernatant.

In embodiments, the magnetic beads are associated with one or morebinding moieties that bind to microorganisms. The one or more bindingmoieties associated with the magnetic beads may identical to thoseassociated with the signaling agents. The one or more binding moietiesassociated with the magnetic beads may be different than thoseassociated with the signaling agents.

In embodiments, the magnetic beads have diameters ranging between 20 nmto 20 microns.

In embodiments, the kit further includes one or more ions or smallmolecules to enhance the binding between the binding moieties and themicroorganism.

In embodiments, the solution comprises <0.15 M salt.

In embodiments, the kit further includes a microorganism binding agent,and wherein the binding moiety binds to the microorganisms indirectlyvia the microorganism binding agent. The binding moiety may beconjugated to streptavidin, neutravidin, or avidin and the microorganismbinding agent may be biotinylated. The binding moiety may be an antibodythat binds to a species specific Fc domain and the microorganism bindingagent may be an antibody capable of binding to the microorganisms withthe species specific Fc domain.

In embodiments, the signaling agent may include one or more of achemiluminophore, a catalyst, or an enzyme. The enzyme may be at leastone of horseradish peroxidase, alkaline phosphatase, acetylcholinesterase, glucose oxidase, beta-D-galactosidase, beta-lactamase,and combinations thereof. The catalyst may be an organometalliccompound.

In embodiments, the signaling agent is provided in a form of ananoparticle, e.g., the signaling agent is encapsulated within ananoparticle. The nanoparticle may be dissociable, which may include ametal oxide; the metal oxide may be or include iron oxide, cesium oxide,and/or cerium oxide.

In embodiments, zero, one, or two washes are performed prior todetermining signal levels.

In embodiments, zero, one, or two washes are performed prior to additionof the signaling agents.

In embodiments, the kit further includes a developer reagent to producea measurable signal.

In embodiments, the one or more reagents include reagents for acatalytic reaction and a reagent that stops the catalytic reaction.

In embodiments, the kit further comprises a device for measuring signal,e.g., an optical and/or electrical signal. The optical measurement maybe fluorescent, time-resolved fluorescent, absorbent, and/orluminescent.

In embodiments, the kit further comprises a multiwell plate, e.g., a24-well, 96-well, 192-well, or 384-well plate.

In embodiments, the further contains instructions for using the kit toperform a herein-disclosed method. The kit may additionally containinstructions for performing steps conducted prior to or subsequent toone or more methods as described herein.

In one embodiment, kits are provided which contain the necessaryreagents to carry out one or more methods as described herein orreagents necessary to carry out steps prior to or subsequent to one ormore methods as described herein.

Treatment Methods

As used herein, the terms “treat,” “treating,” “treatment,” and the likerefer to reducing or ameliorating a disorder and/or a symptom associatedtherewith. It will be appreciated that, although not precluded, treatinga disorder or condition does not require that the disorder, condition orsymptoms associated therewith be completely eliminated. Treating mayinclude a health care professional or diagnostic scientist making arecommendation to a subject for a desired course of action or treatmentregimen, e.g., a prescription.

As used herein, the terms “prevent,” “preventing,” “prevention,”“prophylactic treatment” and the like refer to reducing the probabilityof developing a disorder or condition in a subject, who does not have,but is at risk of or susceptible to developing a disorder or condition.

The term “methods of treating” includes methods of managing, and whenused in connection with the infections microbial organism or infection,includes the amelioration, elimination, reduction, prevention, or otherrelief or management from the detrimental effects of the infectionsmicrobe.

As used herein, the terms “drug”, “medication”, “therapeutic”. “activeagent”, “therapeutic compound”, “composition”, or “compound” are usedinterchangeably and refer to any chemical entity, pharmaceutical, drug,biological, botanical, and the like that can be used to treat or preventa disease, illness, condition, or disorder of bodily function. A drugmay comprise both known and potentially therapeutic compounds. A drugmay be determined to be therapeutic by screening using the screeningknown to those having ordinary skill in the art. A “known therapeuticcompound”, “drug”, or “medication” refers to a therapeutic compound thathas been shown (e.g., through animal trials or prior experience withadministration to humans) to be effective in such treatment. A“therapeutic regimen” relates to a treatment comprising a “drug”,“medication”, “therapeutic”, “active agent”, “therapeutic compound”,“composition”, or “compound” as disclosed herein and/or a treatmentcomprising behavioral modification by the subject and/or a treatmentcomprising a surgical means.

An antimicrobial, e.g., an antibiotic, is an agent capable of killing amicroorganism or inhibiting the growth of a microorganism.

Signaling Agents and Chemical Attachment

In embodiments, the invention features a signaling agent capable ofbinding to the surface of a microorganism. In embodiments, said bindingis non-specific. In embodiments, said binding is specific.

In embodiments, a signaling agent is present during an incubating stepof a method described herein. In embodiments, a signaling agent ispresent after an incubating step of a method described herein.

In embodiments, binding comprises the formation of a covalent bond. Inembodiments, a signaling agent is capable of binding to the surface of amicroorganism, wherein said binding comprises the formation of acovalent bond. In embodiments, a method as described herein results inthe formation of a covalent bond between a group on a microorganismsurface (e.g., via a reactive group such as an electrophilic ornucleophilic group as described herein) and a signaling agent asdescribed herein. In embodiments, a signaling agent has formed acovalent bond to the surface of a microorganism.

In embodiments, binding comprises the formation of a non-covalentinteraction. In embodiments, a signaling agent is capable of binding tothe surface of a microorganism, wherein said binding comprises theformation of a non-covalent interaction. In embodiments, a method asdescribed herein results in the formation of non-covalent interactionbetween a group on a microorganism surface (e.g., via a reactive groupsuch as an electrophilic or nucleophilic group as described herein) anda signaling agent as described herein. In embodiments, a signaling agenthas formed a non-covalent interaction with the surface of amicroorganism.

In embodiments, a non-covalent interaction comprises: ionic interaction,ion-ion interaction, dipole-dipole interaction, ion-dipole interaction,electrostatic interaction, London dispersion, van der Waals interaction,hydrogen bonding, π-π interaction, hydrophobic interaction, or anycombination thereof. In embodiments, a non-covalent interaction is:ionic interaction, ion-ion interaction, dipole-dipole interaction,ion-dipole interaction, electrostatic interaction, London dispersion,van der Waals interaction, hydrogen bonding, π-π interaction,hydrophobic interaction, or any combination thereof.

In embodiments, a non-covalent interaction comprises ionic interactions,van der Waals interactions, hydrophobic interactions, π-π interactions,or hydrogen bonding, or any combination thereof. In embodiments, anon-covalent interaction comprises ionic interaction, van der Waalsinteraction, hydrogen bonding, or π-π interaction, or any combinationthereof.

In embodiments, a signaling agent capable of binding to amicroorganism's surface comprises a group (e.g., a chemical orbiochemical group) capable of binding microorganism membranes, walls,proteins, organelles, saccharides, lipids, cell envelope, or nucleicacids, or any combination thereof. In embodiments, a signaling agentcapable of binding to a microorganism's surface comprises a chemicalgroup (e.g., a nucleophilic group or an electrophilic group) capable ofbinding microorganism membranes, walls, proteins, organelles,saccharides, lipids, cell envelope, or nucleic acids, or any combinationthereof. In embodiments, a signaling agent capable of binding to amicroorganism's surface comprises a biochemical group capable of bindingmicroorganism membranes, walls, proteins, organelles, saccharides,lipids, cell envelope, or nucleic acids, or any combination thereof.

In embodiments, the surface may include a biomolecule to which thesignaling agent binds or associates. Exemplary biomolecules includepeptidoglycans, mureins, mannoproteins, porins, beta-glucans, chitin,glycoproteins, polysaccharides, lipopolysaccharides,lipooligosaccharides, lipoproteins, endotoxins, lipoteichoic acids,teichoic acids, lipid A, carbohydrate binding domains, efflux pumps,other cell-wall and/or cell-membrane associated proteins, other anionicphospholipids, and a combination thereof.

In embodiments, a signaling agent capable of binding to amicroorganism's surface comprises a biochemical group capable of bindingmicroorganism membranes, walls, proteins, organelles, saccharides,lipids, cell envelope, or nucleic acids, or any combination thereof.

In embodiments, a signaling agent capable of binding to amicroorganism's surface comprises a chemical group (e.g., a nucleophilicor electrophilic functional group) capable of binding microorganismmembranes, walls, proteins, organelles, saccharides, lipids, cellenvelope, or nucleic acids, or any combination thereof. In embodiments,said chemical group is a nucleophilic functional group. In embodiments,said chemical group is an electrophilic functional group.

In embodiments, a signaling agent is a biochemical signaling agent. Inembodiments, a biochemical signaling agent comprises a biomolecule suchas an antibody, ligand, protein, aptamer, ss-DNA, ss-RNA, or ss-PNA).

In embodiments, a signaling agent is a chemical signaling agent. Inembodiments, a chemical signaling agent is a chemical compound (e.g., asynthetic chemical compound). In embodiments, a chemical signaling agentdoes not comprise a biomolecule such as an antibody, ligand, protein,aptamer, ss-DNA, ss-RNA, or ss-PNA).

In embodiments, a signaling agent capable of binding to amicroorganism's surface comprises

-   -   a linker group L; and    -   an amplifier group (e.g., an amplifier group 104 that is a        chemical or biochemical amplifier).

In embodiments, an amplifier group is an amplifier group 104, which is achemical or biochemical amplifier. In embodiments, an amplifier group104 is a chemical amplifier. In embodiments, an amplifier group 104 is abiochemical amplifier.

In embodiments, a signaling agent is a chemical compound. Inembodiments, a chemical compound comprises a chemical amplifier groupsuch as those described herein).

In embodiments, a linker group L comprises the conserved (Fc) region ofan antibody.

In embodiments, a linker group L is capable of forming a covalent bondto an amplifier group (e.g., an amplifier group 104 that is a chemicalor biochemical amplifier).

In embodiments, a linker group L forms a covalent bond to a signalamplifier group (e.g., an amplifier group 104 that is a chemical orbiochemical amplifier).

In embodiments, a linker group L is capable of forming one or morenon-covalent interactions to an amplifier group (e.g., an amplifiergroup 104 that is a chemical or biochemical amplifier).

In embodiments, a linker group L forms one or more non-covalentinteractions to an amplifier group (e.g., an amplifier group 104 that isa chemical or biochemical amplifier).

In embodiments, a linker group L comprises a group (e.g., a chemical orbiochemical group) capable of binding a microorganism surface. Inembodiments, a linker group L comprises a group (e.g., a chemical orbiochemical group) that binds a microorganism surface.

In embodiments, a linker group L comprises a group (e.g., a chemical orbiochemical group) that is capable of forming a covalent bond to amicroorganism's surface. In embodiments, a linker group L comprises agroup (e.g., a chemical or biochemical group) that forms a covalent bondto a microorganism's surface.

In embodiments, a linker group L comprises a group (e.g., a chemical orbiochemical group) that is capable of forming one or more non-covalentinteractions with a microorganism's surface. In embodiments, a linkergroup L comprises a group (e.g., a chemical or biochemical group) thatforms one or more non-covalent interactions with a microorganism'ssurface.

In embodiments, a linker group L comprises a chemical moiety 101,wherein said chemical moiety is capable of forming a non-covalentinteraction with the surface of a microorganism. In embodiments, alinker group L comprises a chemical moiety 101, wherein said chemicalmoiety is capable of forming a covalent bond with the surface of amicroorganism. In embodiments, a linker group L comprises a chemicalmoiety 101, wherein said chemical moiety forms a non-covalentinteraction with the surface of a microorganism. In embodiments, alinker group L comprises a chemical moiety 101, wherein said chemicalmoiety forms a covalent bond with the surface of a microorganism.

In embodiments, a linker group L comprises a spacer moiety 102. Inembodiments, spacer moiety 102 is covalently attached to chemical moiety101 and/or to chemical moiety 103. In embodiments, spacer moiety 102 iscovalently attached to chemical moiety 101. In embodiments, spacermoiety 102 is covalently attached to chemical moiety 103. Inembodiments, spacer moiety 102 is covalently attached to chemical moiety101 and to chemical moiety 103. In embodiments, spacer moiety 102 formsa non-covalent interaction with chemical moiety 101 and/or with chemicalmoiety 103. In embodiments, spacer moiety 102 forms a non-covalentinteraction with chemical moiety 101. In embodiments, spacer moiety 102forms a non-covalent interaction with chemical moiety 103. Inembodiments, spacer moiety 102 forms a non-covalent interaction withchemical moiety 101 and with chemical moiety 103.

In embodiments, a linker group L comprises a chemical moiety 103,wherein said chemical moiety is capable of forming a covalent bond to anamplifier group (e.g., an amplifier group 104 that is a chemical orbiochemical amplifier). In embodiments, a linker group L comprises achemical moiety 103, wherein said chemical moiety has formed a covalentbond to an amplifier group (e.g., an amplifier group 104 that is achemical or biochemical amplifier). In embodiments, a linker group Lcomprises a chemical moiety 103, wherein said chemical moiety is capableof forming a non-covalent interaction with an amplifier group (e.g., anamplifier group 104 that is a chemical or biochemical amplifier). Inembodiments, a linker group L comprises a chemical moiety 103, whereinsaid chemical moiety has formed a non-covalent interaction with anamplifier group (e.g., an amplifier group 104 that is a chemical orbiochemical amplifier).

In embodiments, a signaling agent is a chemical compound comprising alinker group L that comprises:

a chemical moiety 101, wherein said chemical moiety is capable offorming a covalent bond or a non-covalent interaction with the surfaceof the microorganisms;

a spacer moiety 102, wherein spacer moiety is covalently attached tochemical moiety 101 and to chemical moiety 103; and

a chemical moiety 103, wherein said chemical moiety has formed or canform a covalent bond to an amplifier group 104 that is a chemical orbiochemical amplifier.

In embodiments, a signaling agent is a chemical compound comprising alinker group L that comprises:

a chemical moiety 101, wherein said chemical moiety is capable offorming a covalent bond or a non-covalent interaction with the surfaceof a microorganism;

a spacer moiety 102, wherein spacer moiety is covalently attached tochemical moiety 101 and to chemical moiety 103; and

a chemical moiety 103, wherein said chemical moiety has formed or canform a non-covalent interaction with an amplifier group 104 that is achemical or biochemical amplifier.

In embodiments, a linker group comprises one chemical moiety 101. Inembodiments, a linker group comprises more than one chemical moiety 101(e.g., a linker group comprises 1, 2, 3, 4, 5, or 6 chemical moieties101).

In embodiments, a linker group comprises one spacer moiety 102. Inembodiments, a linker group comprises more than one spacer moiety 102(e.g., a linker group comprises 1, 2, 3, 4, 5, or 6 spacer moieties102).

In embodiments, a linker group comprises one chemical moiety 103. Inembodiments, a linker group comprises more than one chemical moiety 103(e.g., a linker group comprises 1, 2, 3, 4, 5, or 6 chemical moieties103).

In embodiments, a linker group comprises: one chemical moiety 101, onespacer moiety 102, and one chemical moiety 103. In embodiments, a linkergroup consists of: one chemical moiety 101, one spacer moiety 102, andone chemical moiety 103.

In embodiments, a linker group has the structure of substructure (I):-101-102-103-,  (I)

wherein

“101” represents a chemical moiety 101:

“102” represents a spacer moiety 102; and

“103” represents a chemical moiety 103.

In embodiments, a chemical moiety 101 is capable of forming a covalentbond with the surface of a microorganism.

In embodiments, a chemical moiety 101 is capable of forming a covalentbond with the surface of a microorganism in the presence of one or moreagents that promote coupling (also referred to herein as couplingagents).

In embodiments, agents that promote coupling include glutaraldehyde,formaldehyde, paraformaldehyde,1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC),N,N′-dicyclohexylcarbodiimide (DCC).N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide-methyl-p-toluenesulfonate(CMC), diisopropylcarbodiimide (DIC),(1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium3-oxid hexafluorophosphate) (HATU), Woodward's Reagent, N,N′-carbonyldiimidazole, N-hydroysuccinimide (NHS), or N-hydroxysulfosuccinimide(sulfo-NHS), or any combination thereof.

In embodiments, agents that promote coupling include aldehydes,acrylates, amides, imides, anhydrides, chlorotriazines, epoxides,isocyanates, isothiocyanates, organic acids, monomers, polymers,silanes, or silcates, or any combination thereof.

In embodiments, agents that promote coupling include a carbodiimide, aphosphonium salt, or an ammonium salt, or any combination thereof.

In embodiments agents that promote coupling include glutaraldehyde,N-(3-dimethylaminopropyl)-N′-ethylcarbonate (EDC),(1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium3-oxid hexafluorophosphate) (HATU),(O-benzotriazol-1-yl-N,N,N,N-tetramethyluronium hexafluorophosphate)(HBTU), N-hydroxysuccinimide (NHS), N,N′-dicyclohexylcarbodiimide (DCC),diisopropylcarbodiimide (DIC),hydroxy-3,4-dihydro-4-oxo-1,2,3-benzotriazine (HOOBt),hydroxybenzotriazole (HOBT), 1-hydroxy-7-azabenzotriazole (HOAt),(N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide (EDAC),4-(N,N-dimethylamino)pyridine (DMAP),benzotriazol-1-yloxy-tris(dimethylamino)-phosphonium hexafluorophosphate(BOP), benzotriazol-1-yloxy-tripyrrolidino-phosphoniumhexafluorophosphate (PyBOP), bromo-tripyrrolidino-phosphoniumhexafluorophosphate (PyBrOP),7-aza-benzotriazol-1-yloxy-tripyrrolidinophosphonium hexafluorophosphate(PyAOP), ethylcyano(hydroxyimino)acetato-O2)-tri-(1-pyrrolidinyl)-phosphoniumhexafluorophosphate (PyOxim),3-(diethoxy-phosphoryloxy)-1,2,3-benzo[d]triazin-4(3H)-one (DEPBT),2-(6-chloro-1H-benzotriazol-1-yl)-N,N,N′,N′-tetramethylaminiumhexafluorophosphate (HCTU).N-[(5-chloro-1H-benzotriazol-1-yl)-dimethylamino-morpholino]-uroniumhexafluorophosphate N-oxide (HDMC),1-[1-(cyano-2-ethoxy-2-oxoethylideneaminooxy)-dimethylamino-morpholino]-uroniumhexafluorophosphate (COMU),2-(1-oxy-pyridin-2-yl)-1,1,3,3-tetramethylisothiouroniumtetrafluoroborate (TOTT), tetramethylfluoroformamidiniumhexafluorophosphate (TFFH),N-Ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ),2-propanephosphonic acid anhydride (PPA), triphosgene,1,1′-carbonyldiimidazole (CDI),[(6-nitrobenzotriazol-1-yl)oxy]tris(pyrrolidino)phosphoniumhexafluorophosphate (PyNOP),[[6-(trifluoromethyl)benzotriazol-1-yl]oxy]tris(pyrroli-dino)phosphoniumhexafluorophosphate (PyFOP),[[4-nitro-6-(trifluoromethyl)benzotriazol-1-yl]oxy]tris(pyrrolidino)phosphoniumhexafluorophosphate (PyNFOP),[(6-nitrobenzo-triazol-1-yl)oxy]tris(dimethyl-amino)phosphoniumhexafluorophosphate (NOP), 1-β-naphthalenesulfonyloxy benzotriazole(NSBt), 1-β-naphthalenesulfonyloxy-6-nitrobenzotriazole (N-NSBt),tetramethylfluoroformamidinium hexafluorophosphate (TFFH),bis(tetramethylene)fluoroformamidinium hexafluorophosphate (BTFFH),1,3-dimethyl-2-fluoro-4,5-dihydro-1H-imidazolium hexafluorophosphate(DFIH), Cyanuric chloride (CC), or 2,4-dichloro-6-methoxy-1,3,5-triazine(DCMT), and 2-chloro-4,6-dimethoxy-1,3,5-triazine (CDMT), or anycombination thereof.

In embodiments, agents that promote coupling include EDC, HATU, HBTU,NHS, DCC, HOBT, or PyBOP, or any combination thereof.

In embodiments, agents that promote coupling include EDC, DCC. CMC. DIC,or HATU, or any combination thereof.

In embodiments, agents that promote coupling include glutaraldehyde,formaldehyde, or paraformaldehyde, or any combination thereof.

In embodiments, a chemical moiety 101 is capable of forming anon-covalent interaction with the surface of a microorganism (e.g., anynon-covalent interaction described herein). In embodiments, anon-covalent interaction comprises: ionic, ion-ion, dipole-dipole,ion-dipole, electrostatic, London dispersion, van der Waals, hydrogenbonding, or π-π, or any combination thereof.

In embodiments, a chemical moiety 101 is capable of forming anon-covalent interaction with the surface of a microorganism, whereinsaid non-covalent interaction comprises ionic interactions, van derWaals interactions, hydrophobic interactions, π-π interactions, orhydrogen bonding, or any combination thereof.

In embodiments, a chemical moiety 101 comprises a nucleophilicfunctional group. In embodiments, a chemical moiety 101 comprises agroup formed from a nucleophilic functional group.

In embodiments, a nucleophilic functional group is: amino, amido,hydrazino, hydroxyamino, hydroxy, or thio. In embodiments, anucleophilic functional group is: amino, hydrazino, hydroxyamino, orthio. In embodiments, a nucleophilic functional group comprises: amino,hydrazino, hydroxyamino, hydroxy, or thio. In embodiments, anucleophilic functional group is carboxamide, N-hydroxycarboxamide,carboxyl hydrazide, or guanidino.

In embodiments, a nucleophilic functional group is —NH₂, —NHNH₂,—CONHOH, —CONHNH₂, —ONH₂, —OH, or —SH. In embodiments, a nucleophilicfunctional group is —NH₂, —NHNH₂, —CONHNH₂, or —ONH₂.

In embodiments, a chemical moiety 101 comprises an electrophilicfunctional group.

In embodiments, a chemical moiety 101 comprises a group formed from anelectrophilic functional group.

In embodiments, an electrophilic functional group comprises an aldehyde,a ketone, a carboxylic acid, a carboxylic ester, a carboxylic acidhalide (e.g., acetyl chloride), or a carboxylic acid anhydride (e.g.,acetic anhydride).

In embodiments, an electrophilic functional group comprises an aldehyde,an α-halo ketone, a maleimide, a succinimide, a hydroxysuccinimide, anisothiocyanate, an isocyanate, an acyl azide, a sulfonyl chloride, atosylate ester, a glyoxal, an epoxide, an oxirane, a carbonate, animidoester, an anhydride, a fluorophenyl ester, a hydroxymethylphosphine derivative, a carbonate, a haloacetyl, a chlorotriazine, ahaloacetyl, an alkyl halide, an aziridine, or an acryloyl derivative. Inembodiments, an electrophilic functional group is an aldehyde, an α-haloketone, a maleimide, a succinimide, a hydroxsuccinimide, anisothiocyanate, an isocyanate, an acyl azide, a sulfonyl chloride, atosylate ester, a glyoxal, an epoxide, an oxirane, a carbonate, animidoester, an anhydride, a fluorophenyl ester, a hydroxymethylphosphine derivative, a carbonate, a haloacetyl, a chlorotriazine, ahaloacetyl, an alkyl halide, an aziridine, or an acryloyl derivative.

In embodiments, an electrophilic functional group comprises an aldehyde,an α-halo ketone, a maleimide, a succinimide, or a hydroxysuccinimidegroup.

In embodiments, an electrophilic functional group comprises —CHO,—C(O)CH₂I,

In embodiments, an electrophilic functional group comprises —CHO,—C(O)CH₂I,

In embodiments, chemical moiety 101 comprises a group that is alkyl,alkenyl, alkynyl, phenyl, heteroaryl, haloalkyl, hydroxy, carbonyl, acylhalide, alkoxycarbonyl)oxy, carboxy, haloketone, alkoxy, alkoxyol(hemiacetal or) hemiketal, dialkoxy (e.g., ketal or acetal),trialkoxy(orthoether), carbamoyl, amino, ammonio, imino, imido,succinamido, maleidido, hydroxysuccinamido, biotin, D-Biotin, azido,azo, cyanate, isocyanato, nitroxy, cyano, isocyano, nitrosooxy, nitro,nitroso, oxime, sulfanyl, sulfinyl, sulfonyl, sulfino, sulfo,thiocyanato, isothiocyanato, thioyl, phosphate, or boronate.

In embodiments, spacer moiety 102 is hydrophobic. In embodiments, spacermoiety 102 is hydrophilic.

In embodiments, spacer moiety 102 is peptidic (e.g., derived frompeptide linkages).

In embodiments, spacer moiety 102 comprises inorganic linkages. Inembodiments, spacer moiety 102 comprises organic linkages. Inembodiments, spacer moiety 102 comprises only organic linkages.

In embodiments, spacer moiety 102 is oligomeric. In embodiments, spacermoiety 102 is polymeric. In embodiments, spacer moiety 102 comprisessegments (e.g., 1 to about 300, 1 to about 200, 1 to about 100, 1 toabout 50, 1 to about 25, or 1 to about 10, or 1, 2, 3, 4, 5, 6, 7, 8, 9,or 10 segments) of methylene (—CH₂—), ethylene glycol (—CH₂CH₂O—),iminoethylene (—CH₂CH₂NH—), vinyl alcohol (—CH₂CHOH—)_(x), lactic acid(—CH(CH₃)—C(O)—O—), acrylic acid (—CH₂CH₂(CO₂H)—), methacrylic acid(—CH₂C(CH₃)(CO₂H)—), or methyl methacrylate (—CH₂C(CH₃)(CO₂CH₃)—).

In embodiments, spacer moiety 102 comprises a segment that is

In embodiments, n, m, p, and q independently is an integer of 1 to about300 (e.g., 1 to about 200, 1 to about 100, 1 to about 50, 1 to about 25,or 1 to about 10). In embodiments, each of n, m, p, and q isindependently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In embodiments, spacer moiety 102 comprises

In embodiments, R′ is independently hydrogen or a group that is C₁-C₁₂alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl. In embodiments, o is aninteger of 1 to about 300 (e.g., 1 to about 200, 1 to about 100, 1 toabout 50, 1 to about 25, or 1 to about 10). In embodiments, o isindependently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In embodiments, spacer moiety 102 comprises

In embodiments, R is independently hydrogen or a group that is C₁-C₁₂alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl. In embodiments, r is aninteger of 1 to about 300 (e.g., 1 to about 200, 1 to about 100, 1 toabout 50, 1 to about 25, or 1 to about 10). In embodiments, r isindependently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In embodiments, spacer moiety 102 comprises

In embodiments, R is independently hydrogen or a group that is C₁-C₁₂alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl. In embodiments, s is aninteger of 1 to about 300 (e.g., 1 to about 200, 1 to about 100, 1 toabout 50, 1 to about 25, or 1 to about 10). In embodiments, s isindependently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In embodiments, spacer moiety 102 comprises

In embodiments, t is an integer of 1 to about 300 (e.g., 1 to about 200,1 to about 100, 1 to about 50, 1 to about 25, or 1 to about 10). Inembodiments, t is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In embodiments, spacer moiety 102 comprises:

In embodiments, spacer moiety 102 is a polymer comprising repeatinggroups, comprising alkyl, alkoxy, ester, acrylic, amino, hydroxyl, oracyl hydrazine functional groups, or any combination thereof.

In embodiments, the spacer moiety 102 is:

wherein n, m, p, and q are as defined herein

In embodiments, each of n, m, o, p, q, r, s, or t independently is aninteger of 1 to 100, of 10 to 90, of 10 to 80, of 10 to 70, of 10 to 60,of 10 to 50, of 10 to 40, of 10 to 30, of 10 to 20, or of 1 to 10.

In embodiments, a chemical moiety 103 comprises a group that is anucleophilic functional group.

In embodiments, a chemical moiety 103 comprises a group formed from anucleophilic functional group.

In embodiments, a nucleophilic functional group is: amino, amido,hydrazino, hydroxyamino, hydroxy, or thio. In embodiments, anucleophilic functional group is: amino, hydrazino, hydroxyamino, orthio.

In embodiments, a nucleophilic functional group comprises: amino,hydrazino, hydroxyamino, hydroxy, or thio. In embodiments, anucleophilic functional group is carboxamide, N-hydroxycarboxamide,carboxyl hydrazide, or guanidino.

In embodiments, a nucleophilic functional group is —NH₂, —NHNH₂,—CONHOH, —CONHNH₂, —ONH₂, —OH, or —SH. In embodiments, a nucleophilicfunctional group is —NH₂, —NHNH₂, —CONHNH₂, or —ONH₂.

In embodiments, a chemical moiety 103 comprises a group that is aelectrophilic functional group.

In embodiments, a chemical moiety 103 comprises a group formed from aelectrophilic functional group.

In embodiments, an electrophilic functional group comprises an aldehyde,a ketone, a carboxylic acid, a carboxylic ester, a carboxylic acidhalide (e.g., acetyl chloride), or a carboxylic acid anhydride (e.g.,acetic anhydride).

In embodiments, an electrophilic functional group comprises an aldehyde,an α-halo ketone, a maleimide, a succinimide, a hydroxysuccinimide, anisothiocyanate, an isocyanate, an acyl azide, a sulfonyl chloride, atosylate ester, a glyoxal, an epoxide, an oxirane, a carbonate, animidoester, an anhydride, a fluorophenyl ester, a hydroxymethylphosphine derivative, a carbonate, a haloacetyl, a chlorotriazine, ahaloacetyl, an alkyl halide, an aziridine, or an acryloyl derivative. Inembodiments, an electrophilic functional group is an aldehyde, an α-haloketone, a maleimide, a succinimide, a hydroxysuccinimide, anisothiocyanate, an isocyanate, an acyl azide, a sulfonyl chloride, atosylate ester, a glyoxal, an epoxide, an oxirane, a carbonate, animidoester, an anhydride, a fluorophenyl ester, a hydroxymethylphosphine derivative, a carbonate, a haloacetyl, a chlorotriazine, ahaloacetyl, an alkyl halide, an aziridine, or an acryloyl derivative.

In embodiments, an electrophilic functional group comprises an aldehyde,an α-halo ketone, a maleimide, a succinimide, or a hydroxysuccinimidegroup.

In embodiments, an electrophilic functional group comprises —CHO,—C(O)CH₂I,

In embodiments, an electrophilic functional group comprises —CHO,—C(O)CH₂I,

In embodiments, a chemical moiety 103 comprises a chemical structurethat is carbonyl, alkenyl, alkynyl, hydroxyl, amino, thiol, maleimide,succinimide, hydroxysuccinimide, biotinyl, anhydride, chlorotriazine,epoxide, isocyanate, or isothiocyanate. In embodiments, said group thatis carbonyl, alkenyl, alkynyl, hydroxyl, amino, thiol, maleimide,succinimide, hydroxysuccinimide, biotinyl, anhydride, chlorotriazine,epoxide, isocyanate, or isothiocyanate is capable of forming a covalentbond to an amplifier group (e.g., an amplifier group 104). Inembodiments, said group that is carbonyl, alkenyl, alkynyl, hydroxyl,amino, thiol, maleimide, succinimide, hydroxysuccinimide, biotinyl,anhydride, chlorotriazine, epoxide, isocyanate, or isothiocyanate iscapable of forming non-covalent interaction with an amplifier group(e.g., an amplifier group 104).

In embodiments, a chemical moiety 103 is formed from a chemicalstructure comprising a group that is carbonyl, alkenyl, alkynyl,hydroxyl, amino, thiol, maleimide, succinimide, hydroxysuccinimide,biotinyl, anhydride, chlorotriazine, epoxide, isocyanate, orisothiocyanate. In embodiments, said group that is carbonyl, alkenyl,alkynyl, hydroxyl, amino, thiol, maleimide, succinimide,hydroxysuccinimide, biotinyl, anhydride, chlorotriazine, epoxide,isocyanate, or isothiocyanate has formed a covalent bond to an amplifiergroup (e.g., an amplifier group 104). In embodiments, said group that iscarbonyl, alkenyl, alkynyl, hydroxyl, amino, thiol, maleimide,succinimide, hydroxysuccinimide, biotinyl, anhydride, chlorotriazine,epoxide, isocyanate, or isothiocyanate has formed a non-covalentinteraction with an amplifier group (e.g., an amplifier group 104).

In embodiments, a chemical moiety 103 comprises a group that iscarbonyl, alkenyl, alkynyl, hydroxyl, amino, thiol, maleimide,succinimide, hydroxysuccinimide, or biotinyl.

In embodiments, a chemical moiety 103 comprises a carbonyl, alkenyl,alkynyl, hydroxyl, amino, thiol, maleimide, succinimide,hydroxysuccinimide, or biotinyl functional group.

In embodiments, a chemical moiety 103 comprises:

In embodiments, a chemical moiety 103 comprises a group formed from achemical structure comprising a group that is carbonyl, alkenyl,alkynyl, hydroxyl, amino, thiol, maleimide, succinimide,hydroxysuccinimide, or biotinyl functional group.

In embodiments, a linker group L has the structure of substructure (II):

-   -   wherein

X represents a chemical moiety 101 (e.g., any chemical moiety 101 asdescribed herein;

R represents a spacer moiety 102 (e.g., any spacer moiety 102 asdescribed herein):

Y represents a chemical moiety 103 (e.g., any chemical moiety 103 asdescribed herein); and

each of j and k independently is an integer of 0 to 100.

In embodiments, X is

In embodiments, R is

wherein each of n, m, o, p, q, r, s, or t is as described herein (e.g.,an integer of 1 to about 300).

In embodiments, Y is

In embodiments, X is capable of forming a covalent bond to amicroorganism's surface. In embodiments, X forms a covalent bond to amicroorganism's surface.

In embodiments, X is capable of forming one or more non-covalentinteractions with a microorganism's surface. In embodiments, X forms oneor more non-covalent interactions with a microorganism's surface.

In embodiments, Y is capable of forming a covalent bond to an amplifiergroup 104 (e.g., a chemical or biochemical amplifier). In embodiments, Yforms a covalent bond to an amplifier group such as an amplifier group104 (e.g., a chemical or biochemical amplifier.)

In embodiments, Y is capable of forming one or more non-covalentinteractions to an amplifier group 104 (e.g., a chemical or biochemicalamplifier). In embodiments, Y forms one or more non-covalentinteractions to an amplifier group such as an amplifier group 104 (e.g.,a chemical or biochemical amplifier.)

In embodiments, a linker group L is:

WGA-Biotin, PolymixinB-Biotin, monoclonal antibody, polyclonal antibody,biotinylated monoclonal antibody, biotinylated polyclonal antibody,europium chelate-antibody, horseradish peroxidase-conjugated antibody,and antibody variants (e.g., Fab: fragment, antigen-binding (one arm);F(ab′)2: fragment, antigen-binding, including hinge region (both arms);Fab′: fragment, antigen-binding, including hinge region (one arm); scFv:single-chain variable fragment; di-scFv: dimeric single-chain variablefragment: sdAb: single-domain antibody; Bispecific monoclonalantibodies; trifunctional antibody; and BiTE: bi-specific T-cellengager),

Exemplary amplifier groups include those described in, e.g.,International Publication No. WO 2016/015027 and in InternationalApplication No. PCT/US16/42589, each of which is incorporated byreference in its entirety.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a catalyst, a fluorophore, or a colormetric dye. Inembodiments, an amplifier group (e.g., an amplifier group 104) is acatalyst, a fluorophore, or a colormetric dye.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises an enzyme, a catalyst, or a nanoparticle. In embodiments, anamplifier group (e.g., an amplifier group 104) is an enzyme, a catalyst,or a nanoparticle.

In embodiments, a chemical amplifier group comprises a catalyst, afluorophore, a nanoparticle, or a colormetric dye. In embodiments, achemical amplifier group is a catalyst, a fluorophore, a nanoparticle,or a colormetric dye.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a catalyst. In embodiments, an amplifier group (e.g., anamplifier group 104) is a catalyst.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a fluorophore. In embodiments, an amplifier group (e.g., anamplifier group 104) is a fluorophore. Exemplary fluorophores includethose described in Table 1 of International Application No. PCT/US16/42589, which is incorporated by reference in its entirety.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a colormetric dye. In embodiments, an amplifier group (e.g.,an amplifier group 104) is a colormetric dye.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises an enzyme. In embodiments, an amplifier group (e.g., anamplifier group 104) is an enzyme.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a nanoparticle. In embodiments, an amplifier group (e.g., anamplifier group 104) is a nanoparticle.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a lanthanide.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a lanthanide that is europium, strontium, terbium, samarium,or dysprosium. In embodiments, an amplifier group (e.g., an amplifiergroup 104) comprises a lanthanide selected from the group consisting of:europium, strontium, terbium, samarium, and dysprosium.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises an organic fluorophore.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a fluorophore that is a coordination complex.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a europium coordination complex. In embodiments, acoordination complex is a europium coordination complex. In embodiments,an amplifier group (e.g., an amplifier group 104) comprises a rutheniumcoordination complex. In embodiments, a coordination complex is aruthenium coordination complex. In embodiments, an amplifier group(e.g., an amplifier group 104) comprises a rhenium coordination complex.In embodiments, a coordination complex is a rhenium coordinationcomplex. In embodiments, an amplifier group (e.g., an amplifier group104) comprises a palladium coordination complex. In embodiments, acoordination complex is a palladium coordination complex. Inembodiments, an amplifier group (e.g., an amplifier group 104) comprisesa platinum coordination complex. In embodiments, a coordination complexis a platinum coordination complex.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a chemiluminophore, a quantum dot, an enzyme, an ironcoordination catalyst, a europium coordination complex, a rutheniumcoordination complex, a rhenium coordination complex, a palladiumcoordination complex, a platinum coordination complex, a samariumcoordination complex, a terbium coordination complex, or a dysprosiumcoordination complex.

In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a chemiluminophore. In embodiments, an amplifier group (e.g.,an amplifier group 104) comprises a quantum dot. In embodiments, anamplifier group (e.g., an amplifier group 104) comprises an enzyme. Inembodiments, an amplifier group (e.g., an amplifier group 104) comprisesan iron coordination catalyst. In embodiments, an amplifier group (e.g.,an amplifier group 104) comprises a europium coordination complex. Inembodiments, an amplifier group (e.g., an amplifier group 104) comprisesa ruthenium coordination complex. In embodiments, an amplifier group(e.g., an amplifier group 104) comprises a rhenium coordination complex.In embodiments, an amplifier group (e.g., an amplifier group 104)comprises a palladium coordination complex. In embodiments, an amplifiergroup (e.g., an amplifier group 104) comprises a platinum coordinationcomplex. In embodiments, an amplifier group (e.g., an amplifier group104) comprises a samarium coordination complex. In embodiments, anamplifier group (e.g., an amplifier group 104) comprises a terbiumcoordination complex. In embodiments, an amplifier group (e.g., anamplifier group 104) comprises a dysprosium coordination complex.

In embodiments, an amplifier group 104 comprises a moiety that is:

In embodiments, an amplifier group 104 comprises a moiety that is:

In embodiments, an amplifier group 104 is a catalyst or enzyme. Inembodiments, an amplifier group is horseradish peroxidase, alkalinephosphatase, acetyl cholinesterase, glucose oxidase,beta-D-galactosidase, or beta-lactamase.

In embodiments, amplifier group 104 is horseradish peroxidase.

In embodiments, amplifier group 104 is a fluorophore or colormetric dye.

Suitable fluorophores and colormetric dyes are well known to thoseskilled in the art and are described in The Molecular Probes® Handbook:A Guide to Fluorescent Probes and Labeling Technologies, 11^(th) Ed.(2010) and Gomes. Femandes, and Lima J. Biochem. Biophys. Methods 65(2005) pp 45-80, which are herein incorporated by reference in theirentirety. Exemplary fluorophores also include those described in, e.g.,International Publication No. WO 2016/015027 and in InternationalApplication No. PCT/US16/42589, each of which is incorporated byreference in its entirety.

Examples of suitable fluorophore or colormetric dyes include, but arenot limited to, ethidium bromide, propidium iodide, SYTOX green,phenanthridines, acridines, indoles, imidazoles, cyanine, TOTO, TO-PRO,SYTO, 5-carboxy-2,7-dichlorofluorescein, 5-Carboxyfluorescein (5-FAM),5-Carboxynapthofluorescein, 5-Carboxytetramethylrhodamine (5-TAMRA),5-FAM (5-Carboxyfluorescein), 5-HAT (Hydroxy Tryptamine), 5-ROX(carboxy-X-rhodamine), 6-Carboxyrhodamine 6G, 7-Amino-4-methylcoumarin,7-Aminoactinomycin D (7-AAD), 7-Hydroxy-4-methylcoumarin,9-Amino-6-chloro-2-methoxyacridine, ACMA(9-Amino-6-chloro-2-methoxyacridine), Acridines, Alexa Fluors, Alizarin,Allophycocyanin (APC), AMCA (Aminomethylcoumarin), Bodipy,Carboxy-X-rhodamine, Catecholamine, Fluorescein (FITC), Hydroxycoumarin,Lissamine Rhodamine, Monobromobimane, Oregon Green. Phycoerythrin, SYTO,Thiadicarbocyanine (DiSC3), Thioflavin, X-Rhodamine, C orTetramethylRodamineIsoThioCyanate.

In embodiments, amplifier group 104 is an organometallic compound,transition metal complex, or coordination complex. Exemplary examplesare described in but not limited to EP 0 180 492. EP 0 321 353, EP 0 539435, EP 0 539 477, EP 0 569 496, EP139675, EP64484, U.S. Pat. Nos.4,283,382, 4,565,790, 4,719,182, 4,735,907, 4,808,541, 4,927,923,5,162,508, 5,220,012, 5,324,825, 5,346,996, 5,373,093, 5,432,101,5,457,185, 5,512,493, 5,527,684, 5,534,622. 5,627,074, 5,696,240,6,100,394, 6,340,744, 6,524,727, 6,717,354, 7,067,320, 7,364,597,7,393,599, 7,456,023, 7,465,747, 7,625,930, 7,854,919, 7,910,088,7,955,859, 7,968,904, 8,007,926, 8,012,609, 8,017,254, 8,018,145,8,048,659, 8,067,100, 8,129,897, 8,174,001, 8,183,586, 8,193,174,8,221,719, 8,288,763, 8,362,691, 8,383,249, 8,492,783, 8,632,753,8,663,603, 8,722,881, 8,754,206, 8,890,402, 8,969,862, 9,012,034,9,056,138, 9,118,028, 9,133,205, 9,187,690, 9,193,746, 9,312,496,9,337,432, 9,343,685, 9,391,288, and 9,537,107, which are incorporatedby reference in their entirety. Exemplary organometallic compounds,transition metal complexes, or coordination complexes also include thosedescribed in, e.g., International Publication No. WO 2016/015027 and inInternational Application No. PCT/US 16/42589, each of which isincorporated by reference in its entirety.

In embodiments, amplifier group 104 is a lanthanide coordinationcomplex.

In embodiments, a lanthanide coordination complex is a complex between alanthanide (e.g., Eu or Tb) and a tetradentate ligand.

In embodiments, a lanthanide coordination complex is a complex between alanthanide (e.g., Eu or Tb) and a cryptate ligand.

In embodiments, amplifier group 104 is a coordination complex ofLanthanum (La), Cerium (Ce), Praseodymium (Pr), Neodymium (Pm), Samarium(Sm), Europium (Eu), Gadolinium (Gd), Terbium (Tb), Dysprosium (Dy),Holmium (Ho), Erbium (Er), Thulium (Tm), Ytterbium (Yb), Lutetium (Lu).Ruthenium (Ru), Rhodium (Rh), Palladium (Pd), Osmium (Os), Iridium (Ir),or Platinum (Pt).

In embodiments, amplifier group 104 is a coordination complex of a rareearth metal collectively refers to 17 elements consisting of a group of15 elements from lanthanum having an atomic number of 57 to lutetiumhaving an atomic number of 71 (lanthanides), and two additional elementsconsisting of scandium having an atomic number of 21 and yttrium havingan atomic number of 39. Specific examples of rare earth metals includeeuropium, terbium, lanthanum, cerium, praseodymium, neodymium,promethium, samarium, gadolinium, dysprosium, holmium, erbium, thulium,ytterbium, lutetium, scandium and yttrium, with europium and terbiumbeing preferable, and europium being more preferable.

In embodiments, amplifier group 104 is a coordination complex of alanthanide (e.g., Europium or Terbium) withdiethylenetriaminetetraacetic acid or a cryptate ligand.

In embodiments, amplifier group 104 is a coordination complex of alanthanide (e.g., Europium or Terbium) withdiethylenetriaminetetraacetic acid.

In embodiments, amplifier group 104 is a coordination complex of alanthanide (e.g., Europium or Terbium) with a cryptate ligand.

In embodiments, a signaling agent (e.g., a chemical signaling agent)comprises or is formed from:

In embodiments, a signaling agent may comprise one or more paramagneticmetal chelates in order to form a contrast agent. Preferred paramagneticmetal ions have atomic numbers 21-29, 42, 44, or 57-83. This includesions of the transition metal or lanthanide series which have one, andmore preferably five or more, unpaired electrons and a magnetic momentof at least 1.7 Bohr magneton. Preferred paramagnetic metals includechromium (III), manganese (II), manganese (III), iron (II), iron (III),cobalt (II), nickel (II), copper (II), praseodymium (III), neodymium(III), samarium (III), gadolinium (III), terbium (III), dysprosium(III), holmium (III), erbium (III), europium (III) and ytterbium (III).Additionally, a signaling agent of the present invention may alsocomprise one or more superparamagnetic particles:

In embodiments, a signaling agent may comprise one or more metals thatare included in a metal complex along with or as a part of a fluorescentcompound: The metal complex includes metal complexes having Al, Zn, Be,or the like; a rare-earth metal such as Tb, Eu, or Dy; or a transitionmetal such as Pt or Ir as a central metal, and having an oxadiazole,thiadiazole, phenylpyridine, phenylbenzimidazole, or quinoline structureas a ligand, such as aluminum quinolinol complexes, benzoquinolinolberyllium complexes, benzoxazole zinc complexes, benzothiazole zinccomplexes, azomethyl zinc complexes, porphyrin zinc complexes, andeuropium complexes.

In embodiments, a signaling agent may comprise a luminophore (donor)which features high luminescence quantum efficiency and longluminescence decay time (>100 ns). Preferred luminophores are cationic,metalorganic complexes of palladium, rhodium, platinum, ruthenium,osmium, rare earths (in particular, europium and lanthanum). The organicportion of these metalorganic complexes may consist, for example, ofligands from the group of porphyrins, bipyridyls, phenanthrolines orother heterocyclical compounds.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises an antibody (e.g., monoclonal or polyclonal), modifiedantibodies (e.g., biotinylated monoclonal antibody, biotinylatedpolyclonal antibody, europium chelate-antibody, horseradishperoxidase-conjugated antibody), antibody variants (e.g., Fab: fragment,antigen-binding (one arm): F(ab′)₂: fragment, antigen-binding, includinghinge region (both arms): Fab′: fragment, antigen-binding, includinghinge region (one arm): scFv: single-chain variable fragment; di-scFv:dimeric single-chain variable fragment; sdAb: single-domain antibody;Bispecific monoclonal antibodies: trifunctional antibody; and BiTE:bi-specific T-cell engager), WGA-Biotin, PolymixinB-Biotin, lectin,natural peptide, synthetic peptides, synthetic and/or natural ligands,synthetic and/or natural polymers, synthetic and/or naturalglycopolymers, carbohydrate-binding proteins and/or polymers,glycoprotein-binding proteins and/or polymers, charged small molecules,other proteins, bacteriophages, and/or aptamers.

As used herein, the term “antibody” referrers to any herein-describedtype of antibody, modified antibody, or antibody fragment or type ofantibody, modified antibody, or antibody fragment as known in the art.Thus, “a signaling agent comprising an antibody” includes, as examples,a signaling agent comprising an unmodified monoclonal antibody, a Fabfragment, and a trifunctional antibody.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a lanthanide coordination complex, biotin, antibody,and/or an enzyme.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises or is formed from a structure comprising an antibody,lectin, natural peptide, synthetic peptides, synthetic and/or naturalligands, synthetic and/or natural polymers, synthetic and/or naturalglycopolymers, carbohydrate-binding proteins and/or polymers,glycoprotein-binding proteins and/or polymers, charged small molecules,other proteins, bacteriophages, and/or aptamers.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises an amplifier group 104 that comprises a lanthanidecoordination complex, and/or an enzyme and streptavidin and/or anantibody and/or aptamer.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising a polyclonal and/ormonoclonal antibody.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising a modified antibody.Exemplary modified antibodies include a biotinylated monoclonalantibody, biotinylated polyclonal antibody, a europium chelate-antibody,and a horseradish peroxidase-conjugated antibody.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising an antibody variant.Exemplary antibody variants include Fab: fragment, antigen-binding (onearm); F(ab′)₂, fragment, antigen-binding, including hinge region (botharms): Fab′: fragment, antigen-binding, including hinge region (onearm); scFv: single-chain variable fragment; di-scFv: dimericsingle-chain variable fragment; sdAb: single-domain antibody; Bispecificmonoclonal antibodies; trifunctional antibody: and BiTE: bi-specificT-cell engager).

In embodiments, a signaling agent capable of binding a microorganismsurface comprises WGA-Biotin or PolymixinB-Biotin.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising a synthetic and/or naturalligand and/or peptide.

In embodiments, a ligand and/or peptide is selected frombis(zinc-dipicolylamine), TAT peptide, serine proteases, cathelicidins,cationic dextrins, cationic cyclodextrins, salicylic acid, lysine, andcombinations thereof.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising a synthetic and/or naturalpolymer and/or glycopolymer.

In embodiments, a natural and/or synthetic polymer is linear or branchedand selected from amylopectin,Poly(N-[3-(dimethylamino)propyl]methacrylamide), poly(ethyleneimine),poly-L-lysine, poly[2-(N,N-dimethylamino)ethyl methacrylate], andcombinations thereof.

In embodiments, a natural and/or synthetic polymer and/or glycopolymercomprises moieties including, but not limited to, chitosan, gelatin,dextran, trehalose, cellulose, mannose, cationic dextrans andcyclodextrans, quaternary amines, pyridinium tribromides, histidine,lysine, cysteine, arginine, sulfoniums, phosphoniums, or combinationsthereof including, but not limited to, co-block, graft, and alternatingpolymers.

In embodiments, a signaling agent capable of binding a microorganismsurface comprises a binding moiety comprising a glycoprotein selectedfrom mannose-binding lectin, other lectins, annexins, and combinationsthereof.

In embodiments, a signaling agent capable of binding to a microorganismsurface comprises:

-   -   an antibody; and    -   a europium coordination complex.

In embodiments, a signaling agent capable of binding to a microorganismsurface comprises a linker group L that comprises NH₂—PEG-Biotin (2K),NH₂—PEG-Biotin (4K), sulfo-NHS-Biotin. WGA-Biotin, or polymixinB-Biotin.

In embodiments, a signaling agent capable of binding to a microorganismsurface comprises a Europium complex comprises:

In embodiments, a signaling agent capable of binding to a microorganismsurface comprises a Europium complex comprises:

As disclosed in the below working Examples and throughout theSpecification and Drawings, the present invention provides, at least:

-   -   >89.9% MIC agreement (±1 dilution) between presently-disclosed        methods and CLSI standard with no major/very major errors for        seventy-five strains of twelve bacterial species (including        β-lactams with gram-negative rods);    -   Equivalent MICs between the presently-disclosed method for        direct-from-positive-blood culture and CLSI standard blood        culture sample processing    -   Detection of gram-positive and negative species down to 2×10³        CFU/ml;    -   Non-specific binding of a microorganism by a signaling agent:    -   Use of Europium formulations;    -   Semi-automated device use with data output.

Additional teaching relevant to the present invention are described inone or more of the following: EP139675: EP64484; US 2013/0217063; US2014/0278136: US 2014/0323340: US 2014/0363817: US 2015/0064703; US2015/0337351; US 2016/0010138; U.S. Pat. Nos. 3,798,320; 4,565,790;4,647,536; 4,808,541; 4,927,923; 5,457,185; 5,489,401; 5,512,493;5,527,684; 5,627,074; 5,665,554; 5,695,946; 6,284,470; 6,385,272;6,844,028; 7,341,841; 7,629,029; 7,868,144; 8,178,602; 8,895,255;PCT/US2016/042589: and WO/2016015027 each of which is incorporatedherein by reference in their entireties.

Any of the above aspects and embodiments can be combined with any otheraspect or embodiment as disclosed in the Drawings, in the Summary of theInvention, and/or in the Detailed Description, including the belowExamples.

Although methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention,suitable methods and materials are described below. All publications,patent applications, patents, and other references mentioned herein areincorporated by reference in their entirety. The references cited hereinare not admitted to be prior art to the claimed invention. In addition,the materials, methods, and examples are illustrative only and are notintended to be limiting.

EXAMPLES Example 1 The Present Invention Provides Rapid and AccurateDetermination of an Antimicrobial's Minimum Inhibitory Concentration(MIC)

In this example, the present invention for rapidly determining anantimicrobial's minimum inhibitory concentration (MIC) againstStaphylococcus aureus or Pseudomonas aeruginosa was compared to astandard method requiring an overnight incubation of a S. aureus or P.aeruginosa.

A culture of Staphylococcus aureus (ATCC strain 29213) was grown usingMueller-Hinton (MH) broth overnight at 37° C. with vigorous shaking.Concurrently, two sterile 96-well microplates were prepared with serialdilutions of clindamycin from 32 μg/ml to 0.125 μg/ml and ano-clindamycin control, all in MH broth. The S. aureus concentrationfrom the overnight culture was then set to 5×10⁵ CFU/ml using theMcFarland standard technique for optical density readings at 600 nm. Themicroplates, each well containing 200 μL were inoculated with prepareddilutions of antimicrobial and incubated at 37° C. for 3.5 hours fordetermining antimicrobial susceptibly using a herein-disclosed invention(e.g., the “fast-AST” technique) or incubated at 37° C. overnight (>12hours) for the OD₆₀₀ control. The “fast-AST” microplate was removed fromthe shaking incubator after 4 hours and a horseradish peroxidase (HRP)conjugate of a polyclonal rabbit-anti-S. aureus antibody (FitzgeraldIndustries International, Inc.) was added to each well. The plate wasthen shaken at room temperature for 20 minutes to allow binding, andafterwards, the microplate was centrifuged at 4,000×g in order to pelletthe remaining intact bacteria. The MH broth was then aspirated andsterile broth added for a total of 3 washes. After the final aspiration,a stabilized development solution consisting of3,3′,5,5′-tetramethylbenzidine (TMB) and hydrogen peroxide(ThermoFisher) was added, and the optical density at 650 nm and 450 nmwere monitored for 10 minutes with a microplate reader (Vmax, MolecularDevices). After an overnight incubation, the OD₆₀₀ control microplatewas removed from the incubator, and the optical density at 600 nm wasread directly (Vmax, Molecular Devices). Finally, the MIC was determinedper CLSI standards from the data, as shown in FIG. 5. The MIC determinedby both techniques is the same: 0.125 μg/ml

Similarly, a culture of Pseudomonas aeruginosa (ATCC strain 27853) wasgrown using MH broth overnight at 37° C. with vigorous shaking.Concurrently, two sterile 96-well microplates were prepared with serialdilutions of ceftazidime from 32 μg/ml to 0.125 μg/ml and ano-ceftazidime control, all in MH broth. The P. aeruginosa concentrationfrom the overnight culture was then set to 5×10⁵ CFU/ml using theMcFarland standard technique for optical density readings at 600 nm.These microplates, each well containing 200 μL, were inoculated with theprepared antimicrobial dilutions and incubated at 37° C. for 3.5 hoursfor determining antimicrobial susceptibly using a herein-disclosedinvention or incubated at 37° C. overnight (>12 hours) for the OD₆₀₀control. The “fast-AST” microplate was removed from the shakingincubator after 4 hours and a solution of a horseradish peroxidase (HRP)conjugate of a polyclonal rabbit-anti-P. aeruginosa antibody (Abcam) wasadded to each well. The plate was then shaken at room temperature for 20minutes to allow binding, and afterwards, the microplate was centrifugedat 4,000×g in order to pellet the remaining intact bacteria. The MHbroth was then aspirated and sterile broth added for a total of 3washes. After the final aspiration, a stabilized development solutionconsisting of 3,3′,5,5′-TMB and hydrogen peroxide (ThermoFisher) wasadded, and the optical density at 650 nm and 450 nm were monitored for10 minutes with a microplate reader (Vmax, Molecular Devices). The datashown in FIG. 6 depicts from the 5 minute point after the start ofincubation with detection solution. After an overnight incubation, theOD₆₀₀ control microplate was removed from the incubator, and the opticaldensity at 600 nm was read directly (Vmax, Molecular Devices). Finally,the MIC was determined per CLSI standards from the data, as shown inFIG. 6. The MIC determined by both techniques is the same: 4 μg/ml.

The accuracy of the present invention in determining MIC is clearlydemonstrated in that the slope of the downward region of the data (inFIG. 5 and in FIG. 6) is nearly identical between the present inventionand the overnight cultures.

These data show that the present invention is accurately able todetermine an antimicrobials' MIC which is at least as accurate as astandard method requiring an overnight incubation of a bacterialculture.

Example 2 The Present Invention Provides Rapid and AccurateDetermination of an Antimicrobial's Minimum Inhibitory Concentration(MIC) for Antimicrobial-resistant Bacteria

In this example, the present invention was used to compare the MICs forP. aeruginosa. S. aureus, and E. coli strains that are antimicrobialresistant to, respectively, the MICs for P. aeruginosa, S. aureus, andE. coli strains that are antimicrobial-sensitive.

The MIC for the susceptible P. aeruginosa strain, ATCC 27853, wasdetermined as described in Example 1, with the key difference thatimipenem was used as the antimicrobial (a serial dilution from 32 g/mlto 0.125 μg/ml was used). The MIC for the resistant P. aeruginosastrain, ATCC BAA-2108, was determined similarly. The same 96-wellmicroplate was used for both strains, with 48 wells dedicated to eachstrain. The experiment was repeated 3 times with similar results, andthe resulting data are shown in FIG. 7. The MIC for the susceptiblestrain is 2 μg/ml; the MIC for the resistant strain is 32 μg/ml.

For S. aureus, the same procedure as described above in Example 1 wasused, with the exceptions that methicillin was used as the antimicrobialand a resistant strain, ATCC 43300, was used. For E. coli, the sameprocedure as described above for P. aeruginosa was used, except E. colisusceptible (25922) and resistant (35218) strains were used andampicillin was used as the antimicrobial, and a HRP-conjugate of apolyclonal rabbit-anti-E. coli antibody (Abcam) was used as the chemicalmoiety that allows the signaling agent to bind the bacterium. The“fast-AST” values after a five-minute incubation with detection solutionwere compared with OD₆₀₀ overnight controls, and the data is compiled inFIG. 8.

These data show that the present invention is accurately able todifferentiate an antimicrobial's MIC for a strain of bacteria that isresistant to the antimicrobial and a strain of the same bacteria that issensitive to the antimicrobial.

Example 3 The Present Invention Provides a Detectible Signal atMicrobial Concentration that is Two-hundred Fold Less Concentrated thanis Required for a Standard Method

In this example, the microbial concentration required to provide adetectable signal in present invention for was compared to a standardmethod requiring an overnight incubation of a S. aureus.

S. aureus was cultured overnight as described in Example 1. A serialdilution of the overnight colony was made in a 96-well microplate andthe absorbance was read at 600 nm. These values were compared withMcFarland standards to obtain the bacteria concentration in CFU/ml. Thequantifiable region of the curve is shown, in FIG. 9 (OD₆₀₀); theexperiment was repeated three times with similar results. A similardilution series of S. aureus was treated with S. aureus-specificsignaling agents for 20 min, as described in Example 2. FollowingExample 2's procedure, the microorganisms were centrifuged and washedthree times, and a detection solution was added.

In FIG. 9, the resulting absorbance is shown vs. the McFarlandstandard-determined S. aureus concentration. The “fast-AST” signal isvisible from the starting bacteria concentration of a ClinicalLaboratory Standards Institute (CLSI)-standard AST experiment (i.e.,5×10⁵ CFU/ml), as shown by the arrow. In contrast, the optical signaldoes not enable accurate quantification until ˜10⁸ CFU/ml.

These data show that the present invention is able to provide adetectible and usable signal at microbial culture concentration that istwo-hundred fold less concentration than that required for a standardmethod.

Example 4 The Present Invention Provides MICs Values Similar to thoseObtained from the CLSI Reference Method Across Multiple Species andStrains of Pathogenic Bacteria, Yet in Significantly Less Time thanRequired for the CLSI Method

In this example, the present invention for rapidly determining anantimicrobial's MIC for a plurality of pathogenic bacteria was comparedto the Clinical Laboratory Standards Institute (CLSI) method.

As shown in FIG. 10, MIC determinations for six bacteria were obtainedafter 3.5-hour incubations, whereas the CLSI AST reference methoddeterminations were obtained after sixteen hour incubations (forampicillin-treated cultures) or twenty-four hour incubations (foroxacillin-treated cultures). The drug, signaling agent-chemical moiety(“antibody-HRP conjugate”), and bacteria strains are listed in FIG. 11.A for the signaling agent/chemical moiety, wheat germ agglutinin (WGA)HRP conjugate was used for S. epidermidis testing, and the “fast-AST”assay follows the procedure of Example 2 above. All clinical isolateswere de-identified samples and were sub-cultured a minimum of two timesbefore use. A total of eighty-seven individual samples were tested,including, but not limited to, the following bacterial species: E. coli.S. aureus. P. aeruginosa, K. pneumoniae. E faecalis, Coagulase-NegativeStaphylococci, P. mirabilis, E. faecium, E. clocae, and A. baumannii. Itis noteworthy that the bacterial species tested in this example (exceptP. mirabilis) are together responsible for >90% of positive bloodcultures in many clinical laboratories. Thus, the present invention hasclear clinical relevance to human infectious diseases. The MIC valuesbetween the present invention and the CLSI method are highly similar,yet the present invention requires a three and half hour incubationwhereas the CLSI method requires sixteen hour or twenty-four hourincubations.

These data show that the present invention is accurately able todetermine an antimicrobials' MIC which is at least as accurate as theCLSI method, yet takes significantly less time to determine the MIC;thus, the present invention greatly reduces time before a patient isprovided an appropriate treatment regimen, i.e., a specificantimicrobial and at a particular dosage.

Example 5 With S. aureus and K. pneumoniae Samples, Across a WideVariety of Antimicrobials, the Present Invention Provides MICs ValuesSimilar to those Obtained from the CLSI Reference Method, Yet inSignificantly Less Time

In this example, the present invention was used to rapidly determine aplurality of antimicrobials' MICs when treating S. aureus (agram-positive bacterium) or K. pneumoniae (a gram-negative bacterium)and compared to MIC values obtained by the CLSI method.

Commercial, full-panel dried antimicrobial plates, SensiTitreXR(ThermoFisher) were used in the method of the present invention asdescribed above in Example 2, where bacterial viability was assessed atfour hours. Representative S. aureus and K. pneumoniae results are shownin FIG. 12A to FIG. 12C. There was excellent agreement between MICvalues obtained from the present invention “fast-AST” and theCLSI-obtained results for all experiments except for the erythromycinexperiment with S. aureus and the tetracycline and imipenem experimentswith K. pneumonia; however, according to the FDA, the discrepanciesbetween the present invention and the CLSI results are “minor errors”,see, FIG. 12C.

These data show that the present invention is accurately able todetermine, for two dissimilar bacterial species, a plurality ofantimicrobials' MIC which are at least as accurate as the CLSI method,yet takes significantly less time to determine the MIC; thus, thepresent invention greatly reduces time before a patient is provided anappropriate treatment regimen, i.e., a specific antimicrobial and at aparticular dosage.

Example 6 Using Multiple S. aureus and E. coli Clinical Strains, Acrossa Wide Variety of Antimicrobials, the Present Invention Provides MICsValues Similar to those Obtained from the CLSI Reference Method, Yet inSignificantly Less Time

In this example, the present invention was used to rapidly determine aplurality of antimicrobials' MICs when treating S. aureus (agram-positive bacterium) or E. coli (a gram-negative bacterium) andcompared to MIC values obtained by the CLSI method.

As in Example 5. SensiTitre® plate (ThermoFisher) was used to performthese experiments. The same procedure was used as described in Example2, except 50 μL of inoculum was added to each well, according toThermoFisher's instructions. The CLSI reference method was performed fortwenty-four hours (oxacillin and vancomycin) and eighteen hours(levofloxacin) and for all experiments using the present invention(“fast-AST” method) was performed in four hours (including a three andhalf hour incubation). Results are shown in FIG. 13A to FIG. 13C andFIG. 14A to FIG. 14D. The dark lines in FIG. 13A to FIG. 13C and FIG.14A to FIG. 14D show the CLSI breakpoints for each antimicrobial.Essential Agreement “EA” and Categorical Agreement “CA” are defined asby the FDA in their Class II Guidance Document for Automated ASTSystems. Additionally, for one clinical species of S. aureus, multiple“fast-AST” assays and CLSI standard reference assays, as describedabove, were run over the course of one month to determine consistency ofresults; see FIG. 15.

These data show that the present invention (“fast-AST” procedure)provides consistent results with the CLSI reference method when testedwith multiple antimicrobials on S. aureus and E. coli clinical strains,yet takes significantly less time to determine the MIC; thus, thepresent invention greatly reduces time before a patient is provided anappropriate treatment regimen, i.e., a specific antimicrobial and at aparticular dosage.

Example 7 The Present Invention Provides Rapid and AccurateDetermination of a Plurality of Antimicrobials' MICs for anAntimicrobial-resistant Bacterium

In this example, the present invention was used to determine the MICsfor a plurality of antimicrobials for E. coli strains that areantimicrobial resistant to the MICs for E. coli strains that areantimicrobial-sensitive.

Both Escherichia coli (QC strain, ATCC 25922) and clinical resistant E.coli (“Clinical”) were cultured under standard sterile conditions inMueller-Hinton (MH) broth overnight at 37° C. with shaking. The E. coliconcentration from the overnight culture was then set to 5×10⁵ CFU/mlusing the McFarland standard technique for optical density readings at600 nm. Concurrently, two sterile 96-well microplates were prepared withserial dilutions of a specified antimicrobial (see below) and ano-antimicrobial (saline) control, all in MH broth. The microplates,each well containing 200 μL, were inoculated with the preparedantimicrobial dilutions and incubated at 37° C. for 3 hours, 45 minutesfor determination using the present invention (the “fast-AST”technique). The “fast-AST” microplates were removed from the shakingincubator after 3 hours, 45 minutes and centrifuged for 2.5 minutes at2500 g in order to pellet. The MH broth was then aspirated and 100 μL ofwater was added to each well of both microplates. Then, 10 μL of thechemical moiety (here, Europium-Cryptate formulation) was added to eachwell (to 20 ng/well) and 10 μL of 5% Glutaraldehyde (as the signalingagent) was added to each well. The two microplates were then shaken at300 rpm for 30 minutes. After, both plates were centrifuged for 2.5minutes at 2500 g to pellet. The solution was aspirated and a wash of200 μL PBS-tween was added to each well, followed by a centrifugation topellet. After aspiration of solution, a second identical wash of 200 μLPBS-tween occurred, followed by a final centrifugation to pellet. Theplate was then read using time resolved fluorescence on a BioTek H1plate reader. This process was carried out with the followingantimicrobial preparations: Imipenem at diluted concentrations from 8μg/ml to 0.12 μg/ml (FIG. 16); Ampicillin at diluted concentrations from32 μg/ml to 0.25 μg/ml (FIG. 17); Ceftazidime at diluted concentrationsfrom 32 μg/ml to 0.03 μg/ml (FIG. 18); Gentamicin at dilutedconcentrations from 16 μg/ml to 0.06 μg/ml (FIG. 19); Levofloxacin atdiluted concentrations from 8 μg/ml to 0.06 μg/ml (FIG. 20);Trimethethoprim/Sulfamethoxazole (SXT) at diluted concentrations from 32μg/ml to 0.5 μg/ml (FIG. 21); Ciprofloxacin at diluted concentrationsfrom 4 μg/ml to 0.015 μg/ml (FIG. 22); and Cetriaxone at dilutedconcentrations from 64 μg/ml to 0.12 μg/ml (FIG. 23).

As seen in FIG. 16 to FIG. 23, Escherichia coli (QC strain. ATCC 25922)and the clinical resistant E. coli (“Clinical”) had similar MICs forImipenem, Ceftazidime, Gentamicin, Levofloxacin, Ciprofloxacin, andCetriaxone whereas the two strains had dissimilar MICs for Ampicillinand Trimethethoprim/Sulfamethoxazole (SXT). Accordingly, the data showsthat clinical resistant E. coli strain is resistant to Ampicillin andTrimethethoprim/Sulfamethoxazole (SXT). Thus, if a patient presents withan infection with this (or a similar strain), Ampicillin andTrimethethoprim/Sulfamethoxazole (SXT) should not be administered;instead, Imipenem, Ceftazidime, Gentamicin, Levofloxacin, Ciprofloxacin,and Cetriaxone should be administered.

These data show that the present invention is accurately able todifferentiate an antimicrobial's MIC for a clinically-relevant strain ofbacteria that is resistant to one or more antimicrobials and theantimicrobial's MIC for a strain of the same bacteria that is sensitiveto the antimicrobial; thus, the present invention, in a greatly reducedamount of time relative to standard methods, can provide a patient withan appropriate treatment regimen, i.e., a specific antimicrobial and ata particular dosage.

Example 8 The Present Invention Provides Rapid and AccurateDetermination of a Plurality of Antimicrobials' MICs for anAntimicrobial-sensitive Bacterium

In this example, the present invention was used to determine the MICsfor a plurality of antimicrobials for an S. aureus strain that isantimicrobial sensitive.

S. aureus (QC strain 29213) was cultured under standard sterileconditions in Mueller-Hinton (MH) broth overnight at 37° C. withshaking. The S. aureus concentration from the overnight culture was thenset to 5×10⁵ CFU/ml using the McFarland standard technique for opticaldensity readings at 600 nm. Concurrently, two sterile 96-wellmicroplates were prepared with serial dilutions of a specifiedantimicrobial (see below) and a no-antimicrobial (saline) control, allin MH broth.

The microplates, each well containing 100 μL, were inoculated with theprepared antimicrobial dilutions and incubated at 37° C. for 3 hours, 45minutes for determination using the present invention (the “fast-AST”technique). The “fast-AST” microplates were removed from the shakingincubator after 3 hours, 45 minutes and centrifuged for 2.5 minutes at2500×g in order to pellet. The MH broth was then aspirated and 100 μL of25 mM PBS was added to each well of both microplates. Then, 10 μL of thechemical moiety (here, Europium-Cryptate formulation) was added to eachwell (to 20 ng/well) and 10 μL of 0.005% Glutaraldehyde (as thesignaling agent) was added to each well. The two microplates were thenshaken at 300 rpm for 30 minutes. After, both plates were centrifugedfor 2.5 minutes at 2500×g to pellet. The solution was aspirated and awash of 200 μL PBS-tween was added to each well, followed by acentrifugation to pellet. After aspiration of solution, a secondidentical wash of 200 μL PBS-tween occurred, followed by a finalcentrifugation to pellet, 200 μL PBS-tween was added to each well. Theplate was then read using time resolved fluorescence on a BioTek H1plate reader. This process was carried out with the followingantimicrobial preparations: Vancomycin at diluted concentrations from 32μg/ml to 0.25 μg/ml (FIG. 24); Penicillin at diluted concentrations from8 μg/ml to 0.0625 μg/ml (FIG. 25); and Teicoplanin at dilutedconcentrations from 16 μg/ml to 0.0125 μg/ml (FIG. 26).

As seen in FIG. 24 to FIG. 26, S. aureus (QC strain 29213) the presentinvention determined MICs that were similar to those obtained from astandard CLSI reference method: Vancomycin: 0.5-2 μg/ml; Penicillin:0.25-2 μg/ml and Teicoplanin 0.25-1 μg/ml.

These data show that the present invention is accurately able todetermine a plurality of antimicrobial's MICs; thus, the presentinvention, in a greatly reduced amount of time relative to standardmethods, can provide a patient with an appropriate treatment regimen.i.e., a specific antimicrobial and at a particular dosage.

Example 9 The Present Invention Provides Rapid and AccurateDetermination of an Antimicrobial's MIC Directly from Blood CultureSamples and without the need for Sub-culturing and an Overnight GrowthIncubation

In this example, the present invention was used for rapidly determiningan antimicrobial's MIC directly from a blood culture sample.

One clinical sample for each of E. coli, S. aureus, and K. pneumoniaewere obtained. The isolates were shipped on agar slants, sub-cultured,and stored at −80° C. The samples were removed from the freezer, allowedto warm to room temperature, and streaked on a 5% sheep blood-trypic soyagar (TSA) petri dish (ThermoFisher). The petri dish was placed in anincubator at 35° C. overnight. A single colony was picked and thestreaking process was repeated on a new plate, followed by a second, 35°C. overnight incubation. A total of three to five colonies were pickedand dispersed into 1 mL of sterile saline (Hardy Diagnostics) and theconcentration was determined by optical density measurement at 600 nm(Molecular Devices M2). The sample was diluted in two steps to 2 CFU/mlin 40 mL of sterile cation adjusted Mueller Hinton Broth (MHB, HardyDiagnostics) in a covered flask.

The flask was loaded into a shaker incubator overnight at 35° C. tomimic the performance of a BD BACTEC® blood culture system. The flaskwas put at 4° C. after 10 hours, at which point the E. coliconcentration was determined to be ˜1×10⁸ CFU/ml. This is theapproximate concentration at which commercial blood culture systems,such as the BD BACTEC and bioMerieux BacT/Alert, register positive bloodcultures. The 10-hour incubation time was determined by streaking bloodculture samples on 5% sheep blood TSA-petri dishes, incubating these at35° C. overnight, and determining the colony count.

The sub-culture “control” sample was taken by streaking this “positive”blood culture onto a TSA plate and incubating overnight at 35° C. Astandard CLSI broth microdilution reference method was then performed,as described previously.

Centrifugation-based separation was then performed by following theSepsiTyper (Bruker Daltonics) protocol. Briefly, 1 mL of lysis buffer(Bruker Daltonics) was added to 5 mL of the MHB broth with 1×10⁸ CFU/mlE, coll. The mixture was aliquoted into six microfuge tubes, vortexedfor 10 seconds, and then spun at 13,000 rpm for 2 min. The supernatantwas removed and discarded, 1 mL of washing buffer (Bruker) was added toeach tube, and the tubes were centrifuged at 13,000 rpm for 1 min. Thesupernatant was again removed and discarded. Each pellet was resuspendedin 500 μL of sterile saline by pipetting up-and-down. The solutions weremixed and the bacteria concentration was determined using a PromegaBactitre-Glo™ bacteria cell viability kit.

The samples were diluted into MHB at a concentration of ˜5×10⁵ CFU/ml. A“fast-AST” assay (as described in Example 2) was then performed, and theMIC determinations were compared. The “fast-AST” method on clinicalsamples provided similar MIC values as a standard method which requiressub-culturing, see, FIG. 27 and FIG. 28.

These data show that the present invention (“fast-AST” procedure), whenused directly on clinical samples, provides consistent results with astandard MIC-determining method which requires a sub-culturing stepprior to an overnight growth; thus, the present invention greatlyreduces time before a patient is provided an appropriate treatmentregimen, i.e., a specific antimicrobial and at a particular dosage.

Example 10 Streptavidin Conjugated to Europium Binds to BiotinylatedWheat Germ Agglutinin, which Specifically Binds to Gram PositiveBacteria

In this example, Europium was used as a chemical moiety in signalingagents that comprise wheat germ agglutinin, which specifically binds togram-positive bacteria.

Bacteria (S. aureus) were inoculated across a 96-well plate inconcentrations ranging from 1×10⁵ to 1×10⁹ in MES buffer at pH 6. Toeach well containing the bacteria, and the corresponding control wells,2 μg of biotinylated wheat germ agglutinin (Sigma) was added and thereaction solution was allowed to incubate for 15 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, a commercially-availablestreptavidin-Europium (e.g., from Perkin-Elmer) was added to a finalconcentration per well of 0.4 μg/ml. After incubation for a further 15min, the test plate was centrifuged, using a Thermo Scientific HeraeusMultifuge X3, at a speed of 2500×g for 2.5 minutes in order to pelletthe bacteria in the bottom of the plate while leaving any unassociatedreporter in the supernatant. The plate was then aspirated, using aBioTek Multiflo X plate washer, to remove the supernatant and unreactedreporter, before the addition of wash buffer. This wash procedure wasrepeated two additional times in order to thoroughly remove anyunreacted reporter. Finally, to the aspirated wells, was added thereading buffer before the addition of Delfia Enhancement Solution. Theplate was then incubated for 15 minutes to allow for the europiumenhancement before measurement of the europium using time resolvedfluorescence on a BioTek H1 plate reader, as shown in FIG. 29.

These data show that the use of Europium as a chemical moiety in asignaling agent is accurately able to quantify, bacterial concentrationsin a solution.

Example 11 Streptavidin Conjugated to Europium Binds to BiotinylatedPolymixin B, which Specifically Binds to Gram Negative Bacteria

In this example, Europium was used as a chemical moiety in signalingagents that comprise Polymixin B, which specifically binds togram-negative bacteria.

Bacteria (E. coli) were inoculated across a 96-well plate inconcentrations ranging from 1×10⁵ to 1×10⁹ in MES buffer at pH 6. Toeach well containing the bacteria, and the corresponding control wells,biotinylated polymixin (Hycult Biosciences) was added for a finaldilution of 1:200 and the reaction solution was allowed to incubate for15 minutes in order to facilitate the labeling of the exterior of thebacteria within the well with the chosen reporter. Then, acommercially-available streptavidin-Europium (e.g., from Perkin-Elmer)was added to a final concentration per well of 0.4 μg/ml. Afterincubation for a further 15 min, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated two additional times in order tothoroughly remove any unreacted reporter. Finally, to the aspiratedwells, was added the reading buffer before the addition of DelfiaEnhancement Solution. The plate was then incubated for 15 minutes toallow for the europium enhancement before measurement of the europiumusing time resolved fluorescence on a BioTek H1 plate reader, as shownin FIG. 30.

These data show that the use of Europium as a chemical moiety in asignaling agent is accurately able to quantify bacterial concentrationsin a solution.

Example 12 Europium Detector Provides Larger Signal Range and,therefore, more Accurate MIC Data

This example compared the ability of Europium and HRP, as chemicalmoieties in signaling agents (comprising an antibody that specificallybinds to bacteria) to accurately determining MICs.

Using 96-well plates containing cation-adjusted Mueller Hinton broth andappropriate antimicrobial dilutions, bacteria were prepared by dilutingcolonies into saline to reach a McFarland value of 0.5, which wasverified using a spectrophotometer. This was diluted 1:20 into salineand 10 μl of inoculum was added to each well. Bacterial antimicrobialtesting plates were incubated at 35° C., shaking at 150 rpm for 3 hoursand 45 minutes. After this incubation, cationic magnetic beads andanti-S. aureus antibodies (conjugated to either horseradish peroxidaseor Europium; custom conjugation performed by Cisbio Assays) were addedto each well and incubated for 20 minutes. Using an automated platewasher, magnetic beads were captured and the contents of each well werewashed three times with PBS-Tween20 (0.1%). Then, wells were imageddirectly using time resolved fluorescence (Europium) or TMB was addedand allowed to incubate for 15 minutes, after which the reaction wasstopped by addition of 1 M sulfuric acid and absorbance at 450 nm wasmeasured for each well.

As shown in FIG. 31, using Europium as chemical moiety determined SXT'sMIC more accurately than the MIC determined using HRP as chemicalmoiety.

These data show that the use of Europium as a chemical moiety in asignaling agent is accurately able to determine an antimicrobial's MIC.

Example 13 Embodiments of Europium Formulations, which Non-specificallyLabel Bacteria, are Effective at Detecting Bacteria and QuantifyingBacteria Concentrations

In this example, Europium formulations are non-specifically bound tobacteria.

Bacteria (E. coli) were inoculated across a 96-well plate inconcentrations ranging from 1e5 to 1e9 in MES buffer at pH 6 (EuropiumCryptate-diamine) or HEPES pH 7.5 (EuropiumN1-amino). To each wellcontaining the bacteria, and the corresponding control wells,EuropiumCryptate-diamine (Compound (3); Cisbio) or Europium N1-amino(Compound (6): PerkinElmer) was added at 66 ng/well, then EDC/NHS (at0.1 and 0.3 mg/ml) or glutaraldehyde (0.5% final concentration) wereadded as indicated.

The reaction solution was allowed to incubate for 30 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated one (Eu-Cryptate-diamine) or two(EuropiumN1-amino) additional times in order to thoroughly remove anyunreacted reporter. Wells containing Europium Cryptate-diamine werereconstituted in reading buffer and read using time resolvedfluorescence on a BioTek H1 plate reader, as shown in FIG. 32. Finally,to the aspirated wells treated with Europium Ni-amino, was added thereading buffer before the addition of Delfia Enhancement Solution. Theplate was then incubated for 15 minutes to allow for the europiumenhancement before measurement of the europium using time resolvedfluorescence on a BioTek H1 plate reader, as shown in FIG. 32.

These data show that Europium formulations are accurately able toquantify bacterial concentrations in a solution when the Europiumformulations are non-specifically bound to bacteria.

Example 14 Europium can be Attached to Amines Via Isothiocyanate or toCarboxylic Acids Via NH₂ for Non-specifically Labeling Bacteria whenQuantifying Bacteria Concentrations

In this example, Europium formulations are non-specifically bound tobacteria.

Klebsiella pneumoniae or E. coli were inoculated across a 96-well platein concentrations ranging from 1×10⁵ to 1×10⁹ in MES buffer at pH 6(Europium Cryptate-diamine; Compound (3)) or HEPES pH 7.5 (EuropiumITC;Compound (4)). To each well containing the bacteria, and thecorresponding control wells, Europium Cryptate-diamine (Cisbio) orEuropium ITC (PerkinElmer) was added at 66 ng/well, then EDC/NHS (at 0.1and 0.3 mg/ml) to wells containing Europium Cryptate.

The reaction solution was allowed to incubate for 30 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated one (EuropiumCryptate-diamine) or two(PerkinElmer) additional times in order to thoroughly remove anyunreacted reporter. Wells containing EuropiumCryptate-diamine werereconstituted in reading buffer and read using time resolvedfluorescence on a BioTek H1 plate reader, as shown in FIG. 33. Finally,to the aspirated wells treated with Eu—N1, was added the reading bufferbefore the addition of Delfia Enhancement Solution. The plate was thenincubated for 15 minutes to allow for the europium enhancement beforemeasurement of the europium using time resolved fluorescence on a BioTekH1 plate reader, as shown in FIG. 33.

These data show that Europium formulations are accurately able toquantify bacterial concentrations in a solution when the Europiumformulations are non-specifically bound to bacteria.

Example 15 Glutaraldehyde can be Used to Non-specifically LinkEuropium-Cryptate to the Bacterial Surface

In this example, Europium formulations are non-specifically bound tobacteria with glutaraldehyde.

Klebsiella pneumoniae. E, coli, or Staph aureus were inoculated across a96-well plate in concentrations ranging from 1×10⁵ to 1×10⁹ in MESbuffer at pH 6. To each well containing the bacteria, and thecorresponding control wells, Europium Cryptate-diamine (Compound (3):Cisbio) was added at 66 ng/well, then a 5% solution of glutaraldehyde towells containing Europium Cryptate.

The reaction solution was allowed to incubate for 30 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated once to thoroughly remove any unreactedreporter. Wells containing EuropiumCryptate-diamine were reconstitutedin reading buffer and read using time resolved fluorescence on a BioTekH1 plate reader, as shown in FIG. 34.

These data show that Europium formulations are accurately able toquantify bacterial concentrations in a solution when the Europiumformulations are non-specifically bound to bacteria.

Example 16 EDC/NHS can be Used to Non-specifically CoupleEuropium-Cryptate to the Bacterial Surface

In this example, Europium formulations are non-specifically bound tobacteria with EDC/NHS.

Klebsiella pneumoniae or E. coli were inoculated across a 96-well platein concentrations ranging from 1×10⁵ to 1×10⁹ in MES buffer at pH 6. Toeach well containing the bacteria, and the corresponding control wells,EuropiumCryptate-diamine (Compound (3); Cisbio) was added at 66 ng/well,then EDC/NHS (at 0.1 and 0.3 mg/ml) to wells containing EuropiumCryptate.

The reaction solution was allowed to incubate for 30 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated once to thoroughly remove any unreactedreporter. Wells containing EuropiumCryptate-diamine were reconstitutedin reading buffer and read using time resolved fluorescence on a BioTekH1 plate reader, as shown in FIG. 35.

These data show that Europium formulations are accurately able toquantify bacterial concentrations in a solution when the Europiumformulations are non-specifically bound to bacteria.

Example 17 Effect of Glutaraldehyde Wash Cycles on Non-specifically,Cryptate Labeled Bacteria

In this example, Europium formulations are non-specifically bound tobacteria with various washes comprising glutaraldehyde.

E. coli or Staph aureus were inoculated across a 96-well plate inconcentrations ranging from 1×10⁵ to 1×10⁹ in MES buffer at pH 6. Toeach well containing the bacteria, and the corresponding control wells,EuropiumCryptate-diamine (Compound (3); Cisbio) was added at 66 ng/well,then a 5% solution of glutaraldehyde to wells containing EuropiumCryptate.

The reaction solution was allowed to incubate for 30 minutes in order tofacilitate the labeling of the exterior of the bacteria within the wellwith the chosen reporter. Then, the test plate was centrifuged, using aThermo Scientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5minutes in order to pellet the bacteria in the bottom of the plate whileleaving any unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated twice to investigate the effect ofmultiple washes on overall data quality. Wells containingEuropiumCryptate-diamine were reconstituted in reading buffer and readusing time resolved fluorescence on a BioTek H1 plate reader, as shownin FIG. 36A to FIG. 36C.

These data show that Europium formulations can be non-specifically boundto bacteria using various washes comprising glutaraldehyde.

Example 18 A Two-step Tagging Process Using NH₂-PEG-Biotin Followed byStreptavidin-europium (Eu-SAv) can Non-specifically Label Bacteria

In this example, Europium formulations are non-specifically bound tobacteria using a two-step process.

E. coli was inoculated across a 96-well plate in concentrations rangingfrom 1×10⁵ to 1×10⁹ in MES buffer at pH 6. To each well containing thebacteria, and the corresponding control wells, Amine-PEG-Biotin (LaysanBio) was added at 1 mg/well, then EDC/NHS (at 0.1 and 0.3 mg/ml) towells containing Amine-PEG-Biotin. The reaction solution was allowed toincubate for 15 minutes in order to facilitate the functionalization ofthe exterior of the bacteria within the well with the biotin species. Toeach reaction well, streptavidin-europium (Eu-SAv) (PerkinElmer) wasadded at 400 ng/well. The reaction solution was allowed to incubate for15 minutes in order to facilitate the coupling between the biotin andstreptavidin. Then, the test plate was centrifuged, using a ThermoScientific Heraeus Multifuge X3, at a speed of 2500×g for 2.5 minutes inorder to pellet the bacteria in the bottom of the plate while leavingany unassociated reporter in the supernatant. The plate was thenaspirated, using a BioTek Multiflo X plate washer, to remove thesupernatant and unreacted reporter, before the addition of wash buffer.This wash procedure was repeated twice to investigate the effect ofmultiple washes on overall data quality. Wells containing Eu-SAv werereconstituted in reading buffer and read using time resolvedfluorescence on a BioTek H1 plate reader, as shown in FIG. 37.

These data show that Europium formulations can be non-specifically boundto bacteria using a two-step process comprising NH2-PEG-Biotin followedby Eu-SAv.

Example 19 A Two-step Bacteria Tagging Process with NHS-LC-LC-BiotinFollowed by Eu-SAv can Non-specifically Label Bacteria

In this example, Europium formulations are non-specifically bound tobacteria using another two-step process.

E. coli was inoculated across a 96-well plate in concentrations rangingfrom 1×10⁵ to 1×10⁹ in MES buffer at pH 6. To each well containing thebacteria, and the corresponding control wells, Amine-LC-LC-Biotin(Thermo-Fisher) was added at 1 mg/well, then EDC/NHS (at 0.1 and 0.3mg/ml) to wells containing Amine-PEG-Biotin. The reaction solution wasallowed to incubate for 15 minutes in order to facilitate thefunctionalization of the exterior of the bacteria within the well withthe biotin species. To each reaction well, streptavidin-europium(Perkin-Elmer) was added at 400 ng/well. The reaction solution wasallowed to incubate for 15 minutes in order to facilitate the couplingbetween the biotin and streptavidin. Then, the test plate wascentrifuged, using a Thermo Scientific Heraeus Multifuge X3, at a speedof 2500×g for 2.5 minutes in order to pellet the bacteria in the bottomof the plate while leaving any unassociated reporter in the supernatant.The plate was then aspirated, using a BioTek Multiflo X plate washer, toremove the supernatant and unreacted reporter, before the addition ofwash buffer. This wash procedure was repeated twice to investigate theeffect of multiple washes on overall data quality. Wells containingEuropiumCryptate-diamine were reconstituted in reading buffer and readusing time resolved fluorescence on a BioTek H1 plate reader, as shownin FIG. 38.

These data show that Europium formulations can be non-specifically boundto bacteria using a two-step process comprising NHS-LC-LC-Biotinfollowed by Eu-SAv.

Example 20 Filamentous Bacteria can be Isolated from a Solution Using aFilter System having Pores Ranging in Size from >0.2 Microns to <10Microns; thereby Providing more Accurate Chemical Sensitivity Data

This Example illustrates an embodiment using filtering to excludebacteria that have undergone filamentous growth in response toantimicrobial treatment.

Gram negative rods in particular first undergo filamentous growth inresponse to sub-inhibitory concentrations of cell wall-actingantimicrobials (such as beta lactams). Although these will eventually beinhibited, metabolic “volume” approaches have significant difficulty indistinguishing antimicrobial resistant bacteria from bacteria that haveundergone filamentous growth. When not considered, such filamentousgrowth improperly identifies a bacterium as more resistant than itreally is. Difficulty in determining antimicrobial resistance using a“volume” approach is seen in FIG. 39.

In order to avoid this, in one embodiment, at the end of an incubationperiod, each broth microdilution is loaded into a filter comprising oneor more pre-determined pore sizes (see FIG. 40). The pore sizes arechosen such that a plurality of “normal” bacteria is able to passthrough the filter, but filamentous bacteria greater than a certainlength are trapped. The pore size may be >0.2 microns and <10 microns.

This filter may be designed for parallel sample processing, such as a96-, 384-, or 1586-well plate. A filter may be applied during the ASTprocess, as shown in FIG. 40.

This example further illustrates the key advantage of designing a rapidAST platform that determines intact bacteria presence by surface area asopposed to the conventional metabolic approach, which is essentially avolumetric measurement.

Example 21 Methods for Preparing and Using a Signaling Agent Comprisinga Fluorescent Nanoparticle

In this example, methods for preparing and using a signaling agentcomprising a fluorescent nanoparticle are described.

First, 20 mg of fluorescein dilaurate (FL-DL) were weighed into a clearglass scintillation vial and 1000 mg of Ethanol were added. The FL-DLwas then dissolved in the vial via vortexing. Afterwards, 10 mg ofDSPE-PEG-2 k-amine (Laysan Bio) were added to this mixture and dissolvedby vortexing. Separately, 40 g of DI water was weighed in a beaker, anda stir-bar was added. The beaker was then placed on a magnetic stirrerand stirred at 200 RPM. Next, the Ethanol solution was added to thebeaker in a drop-wise fashion, and the subsequent solution was thenintroduced into a Microfluidics homogenizer and processed one time at6000 psi, 200 gm of DI water was then added to the resulting mixture andTangential Flow Filtration (TFF) was used to purify and concentrate thenanoparticles about 12-fold to 20 mL and were then collected in a glassscintillation vial. This collected nanoparticle formulation was filteredthrough a 0.2 μm filter, and nanoparticle size and concentration weredetermined by NanoSight (Malvern), with an average size reading of 102nm.

The fluorophore-comprising nanoparticles were functionalized withpositively charged small molecules to form a signaling agent useful inthe present invention.

Both Escherichia coli (ATCC 11303) and ampicillin-resistant E. coli(ATCC 39936) were cultured under standard sterile conditions in LB brothat 37° C. Concentrations were determined by measuring absorbance at 600nm (McFarland), and a concentration of 5×10⁵ CFU/ml was set by dilution.Ampicillin was then weighed into sterile water and added in appropriateconcentrations to sterile 3 mL microfuge tubes. Bacteria andnanoparticles at a concentration of 8×10⁸ nanoparticles/ml were bothadded to these ampicillin-coated sterile microfuge tubes. The tubes werethen capped and placed at 37° C. for 1.5 hours with continuous shaking,after which they were opened and each was passed through a 0.2 μmfilter. Next, 100 μL of each filtrate was added to a well of a 96-wellplate and 150 μL of a development solution (5% tetramethylammoniumhydroxide in ethanol) was added to each well. After 5 minutes the platewas read at 490 nm excitation/530 nm emission in a SpectraMax M2microplate reader (Molecular Devices).

FIG. 41 shows the result of an assay using the above-prepared signalingagent comprising a nanoparticle. Here, Escherichia coli andampicillin-resistant E. coli treated with and without 100 μg/mlampicillin, a concentration well above the MIC. An assay for freesignaling agents, which are not associated with intact bacteria, wasperformed after intact bacteria were removed by filtration through a 0.2μm filter. Control groups containing no ampicillin show low fluorescentsignals as does the ampicillin-resistant E. coli group treated withampicillin. The E. coli treated with ampicillin above the MIC show asignificant increase in fluorescence, indicating efficacy of thisantimicrobial.

FIG. 42 shows the result of an assay for E. coli for varying ampicillinconcentrations. The fluorescent signal is low when the ampicillinconcentration is below the MIC, ˜15 μg/ml, and it rises at this value,indicating the efficacy of the antimicrobial in this range

Example 22 The Present Invention can be Performed Using Magnetic Beadsto Isolate Intact Bacteria

In this example, magnetic beads, which are associated with an agentcapable of binging intact bacteria, are used to isolate intact bacteriafrom a solution.

Magnetic beads reactive to E. coli were prepared fromN-hydroxysuccinimidyl ester-activated 1 micron magnetic beads accordingto the manufacturer's instructions (ThermoFisher). Briefly, the suppliedbeads were magnetically captured and the storage solution was aspirated.The beads were then washed with ice-cold 0.1 M hydrochloric acid,followed by the addition of a polyclonal goal-anti-lipopolysaccharide(LPS) antibody (Antibodies-Online Inc.). The reaction was shaken for 2hours, with vortexing every 5 minutes for the first 30 minutes, per themanufacturer's instructions. The beads were then washed thoroughly andstored in phosphate buffered saline, pH 7.4, at 4° C. until use.

Signaling agents comprise a moiety capable of binding to a microorganism(e.g., an antibody that binds to E. coli) and a chemical moiety capableof providing a signal or contributing to production of a signal (e.g.,horseradish peroxidase (HRP)).

The anti-LPS magnetic beads and anti-E. coli signaling agents were addedsimultaneously to a McFarland standard-determined dilution series of E.coli in MH broth. The reaction was allowed to proceed for 20 min,followed by magnetic bead capture with a 96-well microplate magneticstand (V&P Scientific). The wells were washed three times, followed bythe addition of the detection solution described in Example 1. Theoptical densities at 450 nm and 650 nm were read for 10 min. The valueat 5 min is plotted in FIG. 43.

The procedure of Example 1 was then used through the addition ofsignaling agents and functionalized magnetic beads. However, here, theS. aureus strain was ATCC 12600 and three antimicrobials were used:certazidime, oxacillin, and vancomycin.

After the incubation period, magnetic beads with fixed cationic chargesof 0.5 μm size (ChemiCell Fluidmag) were added concurrently with thesignaling agents. The pH was adjusted to ˜8.4 by the addition of 50 μLof borate buffer. The microplate was agitated on an orbital shaker for20 minutes. The microplate was then placed on a magnetic capture platecomprising 24 neodymium N52 magnetics. The MH broth was then aspiratedand PBS with 0.1% Tween-20 added for a total of three washes. After thefinal aspiration, a stabilized development solution consisting of3,3′,5,5′-tetramethylbenzidine (TMB) and hydrogen peroxide(ThermoFisher) was added, and the optical density at 650 nm and 450 nmwere monitored for ten minutes with a microplate reader (Vmax. MolecularDevices). The data shown in FIG. 44 depicts from the five-minute pointafter the start of incubation with detection solution. As expectedincreasing amounts of the antimicrobials, which cause bacterial celllysis, reduces the number of intact bacteria.

These data show that functionalized magnetic particles can captureintact bacteria and enable quantification of the intact bacteria (whenbound to a signaling agent) following an antimicrobial treatment. Suchmagnetic capture may be used together with or in place of otherseparation techniques in order to collect intact bacteria for use in thepresent invention.

Example 23 Centrifugation of Bacterial Solutions Provides more AccurateCounts of Intact Bacteria when Compared to Isolation of Intact Bacteriaby Functionalized Magnetic Beads

In this example, the method for isolating intact bacteria usingfunctionalized magnetic beads (as described in Example 21+) is comparedto a method for isolating intact bacteria using centrifugation.

Capture of intact bacteria using functionalized magnetic beads wasperformed as described above. For the centrifugation data, bacteria werewashed three times by a process of centrifugation at 2500×g for 2.5minutes, manually aspiration, and addition of PBS-Tween. Magnetic beadswere not used for centrifugation washes. Bacteria were treated withvarying concentrations of vancomycin (“VAN”).

FIG. 45 shows that centrifugation provides much higher and more accuratebacterial numbers and MICs than isolation by functionalized magneticbeads.

These data show that centrifugation of bacterial cultures for isolatingintact bacteria is superior to methods using functionalized magneticparticles. Isolation using centrifugation may be used together with(e.g. magnetic isolation) or in place of other separation techniques inorder to collect intact bacteria for use in the present invention.

Example 24 Chemical Amplification Via TAML Nanoparticle Amplifier Allowsfor Signaling with Optimal Sensitivity in the 1×10³ to 1×10⁸ CFU/mlRange Using Standard Optical Detection Equipment

In this example, methods for preparing and using a signaling agentcomprising tetra-amino metalorganic ligand (TAML®) catalysts aredescribed.

Chemical amplification in enabled with a proprietary nanoparticleamplifier, which adapts cutting-edge nanoparticle formulation techniquesfrom drug delivery and a small-molecule catalyst from green chemistry.Each “nanolabel” comprises >6×10⁴ densely packed iron-containing,tetra-amino metalorganic ligand (TAML®) catalysts shielded by a polymershell functionalized with specific ligands (FIG. 46). Each TAML moleculehas molar activities within 5-fold those of horseradish peroxidase, agold-standard immunoassay enzyme label (FIG. 46B). After specificbinding, nanolabels are chemically triggered to release their contentsinto solution, enabling homogeneous catalysis of the optical signal. Thehigh number of catalysts per binding event enables quantification of asfew as 200 intact bacteria (FIG. 46A) and 100-fold sensitivityenhancements over standard enzyme immunoassays (FIG. 46C). In additionto obviating the need for the development of new detection technologies,standard optical detection enables compatibility with standard driedantimicrobial panel microplates, such as SensiTitre plates.

What is claimed is:
 1. A method for determining antimicrobialsusceptibility of microorganisms comprising: incubating a liquidsuspension of microorganisms in the presence of an antimicrobial underconditions that promote growth of the microorganisms, adding a signalingagent that binds to a surface of the microorganisms; separating themicroorganisms bound by the signaling agent from unbound signalingagent; and measuring signal levels associated with the microorganisms ascompared to one or more controls, thereby measuring the antimicrobialsusceptibility of the microorganisms; wherein the signaling agentcomprises a linker group L, and an amplifier group 104 comprises anEuropium coordination complex; and wherein, L forms a covalent bond tothe amplifier group 104; or L forms one or more non-covalentinteractions with an amplifier group
 104. 2. The method of claim 1,wherein the antimicrobial susceptibility of the microorganisms isdetermined in less than 5 hours.
 3. The method of claim 1, whereinadding the signaling agent occurs during the incubating step.
 4. Themethod of claim 1, wherein adding the signaling agent occurs after theincubating step.
 5. The method of claim 1, wherein the linker group Lcomprises: a microorganism binding chemical moiety 101, which forms acovalent bond or a non-covalent interaction with the surface of amicroorganism; a spacer moiety 102, covalently attached to the chemicalmoiety 101 and to another chemical moiety 103; and the chemical moiety103, which forms a covalent or non-covalent interaction with theamplifier group
 104. 6. The method of claim 5, wherein 101 formscovalent bond in the presence of one or more agents that promotecoupling, selected from the group consisting of glutaraldehyde,formaldehyde, paraformaldehyde, EDC, DCC, CMC, DIC, HATU, Woodward'sReagent, N,N′-carbonyl diimidazole, acrylates, amides, imides,anhydrides, chlorotriazines, epoxides, isocyanates, isothiocyanates,organic acids, monomers, polymers, silanes, silcates, NHS, sulfo-NHS,and a combination thereof.
 7. The method of claim 5, wherein chemicalmoiety 101 forms a non-covalent interaction with the surface of amicroorganism, wherein the non-covalent interaction comprises ionicinteractions, van der Waals interactions, hydrophobic interactions, π-πinteractions, or hydrogen bonding, or any combination thereof.
 8. Themethod of claim 5, wherein chemical moiety 101 comprises a nucleophilicfunctional group, wherein said nucleophilic functional group is amino,hydrazino, hydroxyamino, or thiol.
 9. The method of claim 5, whereinchemical moiety 101 comprises an electrophilic functional group, whereinsaid electrophilic functional group comprises an aldehyde, an α-haloketone, a maleimide, a succinimide, a hydroxysuccinimide, anisothiocyanate, an isocyanate, an acyl azide, a sulfonyl chloride, atosylate ester, a glyoxal, an epoxide, an oxirane, a carbonate, animidoester, an anhydride, a fluorophenyl ester, a hydroxymethylphosphine derivative, a carbonate, a haloacetyl, a chlorotriazine, ahaloacetyl, an alkyl halide, an aziridine, an acryloyl derivative,aldehyde, ketone, carboxylic acid, ester, acetyl chloride, or aceticanhydride.
 10. The method of claim 5, wherein spacer moiety 102 ishydrophobic.
 11. The method of claim 5, wherein spacer moiety 102 ishydrophilic.
 12. The method of claim 5, wherein spacer moiety 102 isoligomeric or polymeric, derived from peptide linkages, or comprised ofinorganic linkages.
 13. The method of claim 5, wherein spacer moiety 102comprises a repeating group that is:

wherein, each of n, m, o, p, and q independently is an integer of 1 to300.
 14. The method of claim 5, wherein spacer moiety 102 is


15. The method of claim 5, wherein chemical moiety 103 comprises anucleophilic group.
 16. The method of claim 5, wherein chemical moiety103 comprises an electrophilic group.
 17. The method of claim 5, whereinchemical moiety 103 comprises a group that is carbonyl, alkenyl,alkynyl, hydroxyl, amino, thiol, maleimide, succinimide,hydroxysuccinimide, or biotinyl.
 18. The method of claim 5, whereinchemical moiety 103 comprises a group that is


19. The method of claim 5, wherein chemical moiety 103 is formed from achemical structure comprising a group that is carbonyl, alkenyl,alkynyl, hydroxyl, amino, thiol, maleimide, succinimide,hydroxysuccinimide, biotinyl, anhydride, chlorotriazine, epoxide,isocyanate, or isothiocyanate.
 20. The method of claim 19, wherein saidgroup that is carbonyl, alkenyl, alkynyl, hydroxyl, amino, thiol,maleimide, succinimide, hydroxysuccinimide, or biotinyl forms a covalentbond to the amplifier group 104, or forms a non-covalent bond to theamplifier group
 104. 21. The method of claim 1, wherein linker group Lhas the following structure or is formed from the following structure,

wherein X is

R is

Y is

each of j and k independently is an integer of 0 to 100; and each of n,m, o, p, and q independently is an integer of 1 to
 100. 22. The methodof claim 21, wherein X forms a covalent bond or a non-covalentinteraction with the surface of a microorganism; and/or Y forms acovalent bond to an amplifier group 104 that is a chemical orbiochemical amplifier.
 23. The method of claim 1, wherein said Europiumcoordination complex comprises a structure that is:


24. The method of claim 23, wherein the signaling agent comprises or isformed from a structure selected from the group consisting of:


25. The method of claim 1, wherein the signaling agent comprises: anantibody, lectin, natural peptide, synthetic peptides, bacteriophage,synthetic and/or natural ligands, synthetic and/or natural polymers,synthetic and/or natural glycopolymers, carbohydrate-binding proteinsand/or polymers, glycoprotein-binding proteins and/or polymers, chargedsmall molecules, other proteins, bacteriophages, and/or aptamers. 26.The method of claim 25, wherein the ligand and/or peptide is selectedfrom the group consisting of bis(zinc-dipicolylamine), TAT peptide,serine proteases, cathelicidins, cationic dextrins, cationiccyclodextrins, salicylic acid, lysine, and combinations thereof.
 27. Themethod of claim 25, wherein the natural and/or synthetic polymer islinear or branched and selected from the group consisting ofamylopectin, Poly(N-[3-(dimethylamino)propyl] methacrylamide),poly(ethyleneimine), poly-L-lysine, poly[2-(N,N-dimethylamino)ethylmethacrylate], and combinations thereof.
 28. The method of claim 25,wherein the natural and/or synthetic polymer and/or glycopolymercomprises moieties including, but not limited to, chitosan, gelatin,dextran, trehalose, cellulose, mannose, cationic dextrans andcyclodextrans, quaternary amines, pyridinium tribromides, histidine,lysine, cysteine, arginine, sulfoniums, phosphoniums, or combinationsthereof including, but not limited to, co-block, graft, and alternatingpolymers.
 29. The method of claim 1, wherein multiple antimicrobials aretested in parallel.
 30. The method of claim 1, wherein the determiningsignal levels comprises measuring the signal levels associated withintact microorganisms.
 31. The method of claim 1, wherein the methodfurther comprises a step of determining whether a microorganism isresistant, intermediately resistant or susceptible to one or moreantimicrobials and/or determining one or more antimicrobial minimuminhibitory concentrations (MIC) based upon the signal levels associatedwith intact microorganisms.
 32. The method of claim 1 wherein themicroorganisms are bacteria, fungi, protozoa, or archaea.
 33. The methodof claim 1, wherein the microorganisms are obtained from a biologicalsample from a subject having an infection of the microorganisms and/orare obtained from a culture derived from the biological sample.
 34. Themethod of claim 33, wherein the biological sample is selected from thegroup consisting of blood or blood components, bronchoalveolar lavage,cerebrospinal fluid, nasal swabs, sputum, stool, throat swabs, vaginalswabs, urine, and wound swabs, or a combination thereof.
 35. The methodof claim 1, wherein the one or more controls comprise a positive controlmeasured from microorganisms under otherwise identical conditions butwithout antimicrobials or with one or more antimicrobials for which themicroorganisms are not susceptible.
 36. The method of claim 1, whereinthe one or more controls comprise a control measured from microorganismsunder otherwise identical conditions but without nutrients.
 37. Themethod of claim 1, wherein the one or more controls comprise a controlmeasured from microorganisms under otherwise identical conditions withone or more toxins known to inhibit growth of the microorganisms. 38.The method of claim 1, wherein the separating the microorganisms isperformed by centrifugation, magnetic separation, filtration,electrophoresis, dielectrophoresis, precipitation, agglutination, or acombination thereof.
 39. The method of claim 1, wherein the signal is anoptical signal, an electrical signal, a fluorescent, time-resolvedfluorescent, absorbent, or luminescent signal.
 40. A method fordetermining antimicrobial susceptibility of microorganisms comprising:incubating a liquid suspension of microorganisms in a cartridgecomprising a plurality of chambers, each chamber containing one or moreantimicrobials, under conditions that promote growth of themicroorganisms; adding a signaling agent to the plurality of chambers,wherein the signaling agent binds to a surface of the microorganismsremoving unbound signaling agent; and measuring signaling levels in theplurality of chambers as compared to one or more controls, therebydetermining the susceptibility of microorganisms to the one or moreantimicrobials; wherein the signaling agent comprises a linker group L,and an amplifier group 104 comprises an Europium coordination complex;and wherein, L forms a covalent bond to the amplifier group 104; or Lforms one or more non-covalent interactions with an amplifier group 104.41. The method of claim 40, wherein the antimicrobial susceptibility ofthe microorganisms is determined in less than 5 hours.
 42. The method ofclaim 40, wherein the one or more controls comprise a positive controlmeasured from microorganisms under otherwise identical conditions butwithout antimicrobials or with one or more antimicrobials for which themicroorganisms are not susceptible.
 43. The method of claim 40, whereinthe linker group L comprises: a microorganism binding chemical moiety101, which forms a covalent bond or a non-covalent interaction with thesurface of a microorganism; a spacer moiety 102, covalently attached tothe chemical moiety 101 and to another chemical moiety 103; and thechemical moiety 103, which forms a covalent or non-covalent interactionwith the amplifier group
 104. 44. The method of claim 40, wherein thesignaling agent forms covalent bond with the surface of themicroorganism in the presence of one or more agents that promotecoupling, selected from the group consisting of glutaraldehyde,formaldehyde, paraformaldehyde, EDC, DCC, CMC, DIC, HATU, Woodward'sReagent, N,N′-carbonyl diimidazole, acrylates, amides, imides,anhydrides, chlorotriazines, epoxides, isocyanates, isothiocyanates,organic acids, monomers, polymers, silanes, silcates, NHS, sulfo-NHS,and a combination thereof.
 45. The method of claim 40, wherein themicroorganisms are obtained from a biological sample from a subjecthaving an infection of the microorganisms and/or obtained from a culturederived from the biological sample; and wherein the biological sample isselected from the group consisting of blood or blood components,bronchoalveolar lavage, cerebrospinal fluid, nasal swabs, sputum, stool,throat swabs, vaginal swabs, urine, and wound swabs, or a combinationthereof.